-
Notifications
You must be signed in to change notification settings - Fork 0
Expand file tree
/
Copy pathsearch.xml
More file actions
2084 lines (1993 loc) · 272 KB
/
search.xml
File metadata and controls
2084 lines (1993 loc) · 272 KB
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
<?xml version="1.0" encoding="utf-8"?>
<search>
<entry>
<title>BLAST及NT库本地化</title>
<url>/2023/04/16/BLAST%E5%8F%8ANT%E5%BA%93%E6%9C%AC%E5%9C%B0%E5%8C%96/</url>
<content><![CDATA[<p>下载NCBI的NT数据库到服务器本地<br>Blast比对结果中输出物种信息<br>用TaxonKit、blastdbcmd、makeblastdb建立子库 </p>
<span id="more"></span>
<h1 id="NT库本地化"><a href="#NT库本地化" class="headerlink" title="NT库本地化"></a>NT库本地化</h1><h2 id="下载文件"><a href="#下载文件" class="headerlink" title="下载文件"></a>下载文件</h2><ol>
<li><p>可选文件格式</p>
<ol>
<li>blast index文件<br> <code>https://ftp.ncbi.nlm.nih.gov/blast/db</code>中的nt.*.tar.gz 。<br> 下载完成后,MD5验证,解压文件,就可以直接用于blast。index中已经包含物种Taxonomy信息。但是压缩包中没有Fasta文件,需要的话可以用blastdbcmd提取。</li>
<li>Fasta文件<br><code>https://ftp.ncbi.nlm.nih.gov/blast/db/FASTA</code>中的nt.gz 。<br>下载完成并解压后,需要自建blast index;如果结果中还需要物种Taxonomy信息,建index前还需要准备好TaxIDMapFile文件。</li>
</ol>
</li>
<li><p>下载blast index文件<br> wget下载有点问题,不知道是服务器还是网络问题,wget下载的文件总是MD5校验失败;有时候重新下又能校验成功。<br> aspera下载不行,链接NCBI失败,可能是必须开放某个指定端口。<br> 最后是用的rsync下载。 </p>
<ol>
<li>文件列表下载 <figure class="highlight plaintext"><table><tr><td class="code"><pre><span class="line">rsync --no-motd --files-from=<文件列表> <文件源> <下载存放路径></span><br><span class="line"># 示例</span><br><span class="line">rsync --no-motd --files-from=***/File.list rsync://ftp.ncbi.nlm.nih.gov/blast/db/ ***/NT_Database</span><br></pre></td></tr></table></figure>
File.list(每个文件1列)<br> <img src="https://pic.imgdb.cn/item/643c01890d2dde57770d7686.jpg" alt="File.list"></li>
</ol>
<ul>
<li>实际下载文件路径是<文件源>加上File.list中的内容,完整路径如:rsync://ftp.ncbi.nlm.nih.gov/blast/db/nt.22.tar.gz。</li>
<li>当File.list中的内容包含子目录,<下载存放路径>中会自动生成对应层级目录,例如File.list中的内容是“blast/db/nt.22.tar.gz”,则下载的nt.22.tar.gz会保存在<code><下载存放路径>/blast/db</code>中。</li>
</ul>
<ol start="2">
<li>并行下载<br> 推荐这种方式,文件列表逐个下载太慢,这个每行加“&”后台并行下载文件比较快。 <figure class="highlight plaintext"><table><tr><td class="code"><pre><span class="line">rsync --no-motd <文件源> <下载存放路径></span><br><span class="line"># 示例</span><br><span class="line">rsync --no-motd rsync://ftp.ncbi.nlm.nih.gov/blast/db/nt.22.tar.gz ***/NT_Database &</span><br><span class="line">rsync --no-motd rsync://ftp.ncbi.nlm.nih.gov/blast/db/nt.23.tar.gz ***/NT_Database &</span><br></pre></td></tr></table></figure></li>
</ol>
</li>
</ol>
<h2 id="MD5验证"><a href="#MD5验证" class="headerlink" title="MD5验证"></a>MD5验证</h2><p><code>https://ftp.ncbi.nlm.nih.gov/blast/db</code>中还有nt.*.tar.gz.md5文件,用于MD5验证。<br>全部nt.<em>.tar.gz和nt.</em>.tar.gz.md5文件都下载完后,md5文件合并一起验证。<br>nt.all.md5.check中,文件名后是OK即文件完整;如果是Fail,则不完整,需要重新下载该文件。 </p>
<figure class="highlight plaintext"><table><tr><td class="code"><pre><span class="line"># 合并所有md5文件</span><br><span class="line">cat nt.*.tar.gz.md5 > nt.all.md5</span><br><span class="line"># md5验证</span><br><span class="line">md5sum -c nt.all.md5 > nt.all.md5.check</span><br></pre></td></tr></table></figure>
<h2 id="解压文件"><a href="#解压文件" class="headerlink" title="解压文件"></a>解压文件</h2><p><code>tar -zxvf nt.*.tar.gz</code><br>解压后,nt.*.tar.gz文件删除或者备份都可以。<br>一般是删除?除了需要迁移到别的服务器,好像也没有能再用到的地方了。 </p>
<h2 id="Blast比对"><a href="#Blast比对" class="headerlink" title="Blast比对"></a>Blast比对</h2><p>blast结果中Subject Seq-id(NT库的序列ID)格式为“gi|384474605|emb|HE793683.1|”,含有<a href="https://www.ncbi.nlm.nih.gov/genbank/sequenceids/">GI numbers</a>和<a href="https://support.nlm.nih.gov/knowledgebase/article/KA-03436/en-us">GenBank accession numbers</a>;不包含Taxid信息。<br>如果blast index中有Taxonomy信息,可以在输出格式增加staxids sscinames,使结果额外输出物种的Taxid和物种名称。 </p>
<figure class="highlight plaintext"><table><tr><td class="code"><pre><span class="line"># Shell</span><br><span class="line"></span><br><span class="line">sample="Input"</span><br><span class="line">query_fa="Input.fa"</span><br><span class="line"></span><br><span class="line">database="<NT库目录>/nt"</span><br><span class="line">identity="98"</span><br><span class="line">cov_hsp="90"</span><br><span class="line">evalue="1e-5"</span><br><span class="line"></span><br><span class="line">threads="8"</span><br><span class="line"></span><br><span class="line"># 如果不export BLASTDB的话,要在bashrc声明BLASTDB,否则报错</span><br><span class="line"># 在-outfmt添加staxids sscinames,使结果额外输出物种Taxid、物种名称</span><br><span class="line">export BLASTDB=<NT库目录> && blastn -query ${query_fa} -db ${database} -out ${sample}.noheader -outfmt "6 qaccver saccver pident length mismatch gapopen qstart qend sstart send evalue bitscore staxids sscinames stitle" -num_threads ${threads} -evalue ${evalue} -perc_identity ${identity} -qcov_hsp_perc ${cov_hsp}</span><br><span class="line"></span><br><span class="line"># 表头</span><br><span class="line">echo -e "Query Seq-id\tSubject Seq-id\tIdentity\tAlignment length\tMismatch\tGap Open\tQuery Start\tQuery End\tSubject Start\tSubject End\tEvalue\tBitscore\tTaxonomy ID\tScientific Name\tSeq Title" > ${sample}.tsv</span><br><span class="line"></span><br><span class="line"># 合并blast结果和表头</span><br><span class="line">cat ${sample}.noheader >> ${sample}.tsv</span><br><span class="line"></span><br><span class="line"># 删除没有表头的blast结果</span><br><span class="line">rm -f ${sample}.noheader</span><br></pre></td></tr></table></figure>
<h1 id="构建子库"><a href="#构建子库" class="headerlink" title="构建子库"></a>构建子库</h1><ul>
<li>用blastdbcmd可以根据Taxid从NT库抽取相关序列,从而构建子库。 </li>
<li>用<a href="https://bioinf.shenwei.me/taxonkit/">TaxonKit</a>可以获取某个Taxid节点以下所有Taxid,也就是说不止可以抽取单个物种的序列,还可以提供Taxid列表来抽取整个目、科、属…的序列。 </li>
<li>TaxonKit需要<a href="https://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz">taxdump.tar.gz</a>。NT库和taxdump.tar.gz最好日期一致,因为Taxonomy会更新,可能导致NT库的Taxid和TaxonKit提取的有区别。具体见TaxonKit的<a href="https://bioinf.shenwei.me/taxonkit/chinese/#taxid-changelog-taxid">TaxID changelog</a>。 </li>
<li>如果要用Taxid统计blast结果中的物种信息,需要注意有些亚种/株的Taxid与物种(Species)等级Taxid不一样。如Streptococcus parasanguinis ATCC 903(Taxid 888048)的Rank是strain;它是属于Streptococcus parasanguinis(Taxid 1318)这个物种的。用taxonkit lineage可以获取某个Taxid在物种等级的名称和Taxid。如<code>echo 888048 | taxonkit lineage | taxonkit reformat -t -f \"{s}\" | cut -f 3,4</code>。 </li>
<li>用子库作为参考序列blast时,将-db参数换成{Index_Dir}/${Name}.fa即可。</li>
</ul>
<p>以链球菌属举例,在NCBI的<a href="https://www.ncbi.nlm.nih.gov/taxonomy">Taxonomy数据库</a>可以找到Streptococcus的Taxid是1301。 </p>
<figure class="highlight plaintext"><table><tr><td class="code"><pre><span class="line"># Shell</span><br><span class="line"></span><br><span class="line">Name="Streptococcus"</span><br><span class="line">Taxid="1301"</span><br><span class="line">Index_Dir="Streptococcus_Index"</span><br><span class="line"></span><br><span class="line"># 获取该Taxid节点以下所有子节点的Taxid</span><br><span class="line">taxonkit list -I "" --ids $Taxid > ${Index_Dir}/${Name}.taxid</span><br><span class="line"></span><br><span class="line"># 提取相关序列</span><br><span class="line">blastdbcmd -db <NT库目录>/nt -taxidlist ${Index_Dir}/${Name}.taxid > ${Index_Dir}/${Name}.fa</span><br><span class="line"></span><br><span class="line"># 提取GenBank accession numbers(GI号也可以)和Taxid的对应关系文件</span><br><span class="line">blastdbcmd -db <NT库目录>/nt -taxidlist ${Index_Dir}/${Name}.taxid -outfmt "%a %T" > ${Index_Dir}/taxid_map.txt</span><br><span class="line"></span><br><span class="line"># 建blast index,通过-parse_seqids -taxid_map在index中附加物种Taxonomy信息</span><br><span class="line">makeblastdb -dbtype nucl -in ${Index_Dir}/${Name}.fa -out ${Index_Dir}/${Name}.fa -parse_seqids -taxid_map ${Index_Dir}/taxid_map.txt</span><br><span class="line"></span><br><span class="line"># 提取序列的GenBank accession numbers、Taxid、物种名称(比对用不上,就是看看参考里有什么)</span><br><span class="line">blastdbcmd -db <NT库目录>/nt -taxidlist ${Index_Dir}/${Name}.taxid -outfmt "%a %T %S" > ${Index_Dir}/${Name}.Name.tsv</span><br></pre></td></tr></table></figure>
<p>taxid_map.txt(第1列GenBank accession numbers,第2列Taxid)<br><img src="https://pic.imgdb.cn/item/643c01cc0d2dde57770dcff5.jpg" alt="taxid_map.txt"><br>Name.tsv(第1列GenBank accession numbers,第2列Taxid,第3列物种名称)<br><img src="https://pic.imgdb.cn/item/643c01b20d2dde57770dad98.jpg" alt="Name.tsv"> </p>
<h1 id="假如用nt-gz建库"><a href="#假如用nt-gz建库" class="headerlink" title="假如用nt.gz建库"></a>假如用nt.gz建库</h1><ul>
<li>nt.gz解压后是NT库的fasta文件。如果不需要物种信息的话,直接makeblastdb建库就行。如果balst结果要有物种信息,则需要提供GenBank accession numbers和Taxid对应关系,类似上面的子库构建的-parse_seqids -taxid_map方式。 </li>
<li>GenBank accession numbers和Taxid对应关系文件可以用<a href="https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/nucl_gb.accession2taxid.gz">nucl_gb.accession2taxid.gz</a>。和taxdump.tar.gz一样原因,accession2taxid最好与NT库日期一致。 </li>
<li>nucl_gb.accession2taxid.gz格式是tsv,第一列Accession,第二列Accession.version,第三列TaxId,第四列GI;整理成taxid_map格式后,用makeblastdb加-parse_seqids -taxid_map建库就行。</li>
</ul>
<h1 id="一些blastn参数"><a href="#一些blastn参数" class="headerlink" title="一些blastn参数"></a>一些blastn参数</h1><p>-task:默认是megablast,可选blastn、blastn-short、dc-megablast、megablast、rmblastn<br>-query:需要比对的fasta序列<br>-db:数据库路径,写到fasta前缀为止,如***/NT_Database/nt<br>-out:输出文件<br>-outfmt:输出格式,6是tab分割且无表头的格式,其他格式见blastn帮助文档<br>-num_threads:线程数,默认1;与-mt_mode相关,具体见<a href="https://www.ncbi.nlm.nih.gov/books/NBK571452/">这里</a><br>-evalue:e值过滤阈值,默认10<br>-perc_identity:identity百分比过滤阈值,取值0 ~ 100<br>-qcov_hsp_perc:hsp覆盖度百分比过滤阈值,取值0 ~ 100<br>-max_target_seqs:输出结果保留多少比对上的subject序列,默认500,建议大于等于5<br>-max_hsps:每个query序列比对上的每个subject序列保留多少个HSP,需要填写大于等于1,无默认值 </p>
]]></content>
<categories>
<category>Log</category>
</categories>
<tags>
<tag>NT</tag>
<tag>BLAST</tag>
<tag>数据库</tag>
<tag>TaxonKit</tag>
</tags>
</entry>
<entry>
<title>BLAST短序列比对没有结果</title>
<url>/2023/08/03/BLAST%E7%9F%AD%E5%BA%8F%E5%88%97%E6%AF%94%E5%AF%B9%E6%B2%A1%E6%9C%89%E7%BB%93%E6%9E%9C/</url>
<content><![CDATA[<p>BLAST短序列比对hg19,没有比对结果。需要设置特定参数。</p>
<span id="more"></span>
<h1 id="运行环境、问题说明"><a href="#运行环境、问题说明" class="headerlink" title="运行环境、问题说明"></a>运行环境、问题说明</h1><ul>
<li>版本:ncbi-blast-2.14.0+</li>
<li>模块:blastn</li>
<li>参考:blast db是用hg19建的</li>
<li>问题:比对引物序列(21~23 nt)没有结果,没有任何报错信息</li>
<li>测试:比对稍微长点的序列(130 nt)有结果</li>
<li>测试:同样的引物短序列在UCSC的BLAT有比对结果</li>
</ul>
<h1 id="解决方法"><a href="#解决方法" class="headerlink" title="解决方法"></a>解决方法</h1><h2 id="简单说明"><a href="#简单说明" class="headerlink" title="简单说明"></a>简单说明</h2><p>blastn比对短序列,要设置这3个参数: </p>
<ul>
<li>-dust必须设置成no,否则可能没有结果</li>
<li>-word_size设置成query序列长度的1/2</li>
<li>-evalue设置大一点,例如1000,否则可能会漏掉部分结果</li>
</ul>
<h2 id="详细说明"><a href="#详细说明" class="headerlink" title="详细说明"></a>详细说明</h2><h3 id="参考1"><a href="#参考1" class="headerlink" title="参考1"></a>参考1</h3><p><a href="https://bioinformatics.stackexchange.com/questions/4226/blastn-no-hits-found#:~:text=The%20way%20blast%20works%20is%20%28simplifying%20a%20bit%29,word%20size%2C%20no%20match%20will%20ever%20be%20found">BLAST(n): No hits found</a> </p>
<figure class="highlight plaintext"><table><tr><td class="code"><pre><span class="line">1. Masking</span><br><span class="line">Blast will mask low complexity regions by default. Since your sequence is nothing but Gs, it is a safe bet that it is being masked, so no hits will be found for it.</span><br><span class="line">2. Score/e-value thresholds</span><br><span class="line">Another source of complication is that even if a match is found, that match will have very bad scores. Both the actual score of the alignment and the e-value will be very bad. Since this is such a simple sequence, it will always score badly.</span><br><span class="line">3. Word-size</span><br><span class="line">The way blast works is (simplifying a bit) by finding a match for N residues (the word size) and then extending that match if extending increases the score. If your query sequence is shorter than the word size, no match will ever be found.</span><br></pre></td></tr></table></figure>
<p>以上3个可能原因:</p>
<ol>
<li>不是,query序列不是低复杂度序列</li>
<li>不是,测试了-evalue 1、-evalue 10,没结果</li>
<li>不是,测试了-word_size 4,没结果</li>
</ol>
<h3 id="参考2(建议仔细看这个)"><a href="#参考2(建议仔细看这个)" class="headerlink" title="参考2(建议仔细看这个)"></a>参考2(建议仔细看这个)</h3><p><a href="https://web.cas.org/help/BLAST/topics/shrt_seq.htm">Searching Short Sequences</a><br>参考2的操作说明针对的是在线版本的blast;软件对应的参数就是这3个,具体说明看<code>blastn -help</code>。 </p>
<p>最终设置如下3个参数,可以比对出大部分query: </p>
<ul>
<li><p>-dust no</p>
<ul>
<li>是否用DUST算法过滤query序列,调用的应该是dustmasker。默认是开启DUST的,默认参数是level 20 window 64 linker 1。</li>
<li>可能是在这个window参数下,我的query太短了,所以都被滤掉了,其实根本没有进行比对,所以只设置-word_size是无效的?</li>
</ul>
</li>
<li><p>-word_size 11</p>
<ul>
<li>word_size我的理解可能是相当于比对起始的种子序列长度?</li>
<li>blastn的help里只写了需要≥4,没写默认是多少。</li>
<li>参考2里说blastn默认的word_size是11,但是测试了不设置word_size时没有结果,设置为11时有结果。</li>
<li>参考2里说可以调小word_size,但建议最小是query长度的1/2。</li>
<li>测试了4和11都有结果,4会慢很多。6线程,4跑了9m57.677s,11跑了0m1.174s。</li>
</ul>
</li>
<li><p>-evalue 1000</p>
<ul>
<li>看到有些结果的Evalue是0.003,如果设置-evalue 1e-5会漏掉这部分结果</li>
</ul>
</li>
</ul>
<h1 id="参考代码"><a href="#参考代码" class="headerlink" title="参考代码"></a>参考代码</h1><figure class="highlight plaintext"><table><tr><td class="code"><pre><span class="line">sample="Test"</span><br><span class="line">query_fa="Input.fa"</span><br><span class="line">threads="6"</span><br><span class="line"></span><br><span class="line">database="/xxxx/balst_db"</span><br><span class="line"></span><br><span class="line">identity="98"</span><br><span class="line">cov_hsp="95"</span><br><span class="line"></span><br><span class="line"># Long Query Sequence</span><br><span class="line"># blastn -query $query_fa -db $database -out ${sample}.noheader -outfmt "6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore" -num_threads $threads -perc_identity $identity -qcov_hsp_perc $cov_hsp -evalue 1e-5</span><br><span class="line"></span><br><span class="line"># Short Query Sequence</span><br><span class="line">blastn -query $query_fa -db $database -out ${sample}.noheader -outfmt "6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore" -num_threads $threads -perc_identity $identity -qcov_hsp_perc $cov_hsp -evalue 1000 -dust no -word_size 11</span><br><span class="line"></span><br><span class="line">echo -e "Query Seq-id\tSubject Seq-id\tIdentity\tAlignment length\tMismatch\tGap Open\tQuery Start\tQuery End\tSubject Start\tSubject End\tEvalue\tBitscore" > ${sample}.tsv</span><br><span class="line"></span><br><span class="line">cat ${sample}.noheader >> ${sample}.tsv</span><br><span class="line"></span><br><span class="line">rm -f ${sample}.noheader</span><br></pre></td></tr></table></figure>]]></content>
<categories>
<category>Bug</category>
</categories>
<tags>
<tag>BLAST</tag>
<tag>Mapping</tag>
<tag>比对</tag>
</tags>
</entry>
<entry>
<title>Bam文件操作</title>
<url>/2023/05/22/Bam%E6%96%87%E4%BB%B6%E6%93%8D%E4%BD%9C/</url>
<content><![CDATA[<p>用Linux命令行或软件对Bam文件进行操作</p>
<span id="more"></span>
<h1 id="统计CIGAR,从多到少排序"><a href="#统计CIGAR,从多到少排序" class="headerlink" title="统计CIGAR,从多到少排序"></a>统计CIGAR,从多到少排序</h1><figure class="highlight plaintext"><table><tr><td class="code"><pre><span class="line">sambamba view -F "ref_name=='******' and not secondary_alignment and not supplementary" ******.bam | cut -f 6 | sort | uniq -c | sed -r 's/^\s+//' | sed -r 's/\s+/\t/' | sort -k 1 -nr > CIGAR.tsv</span><br></pre></td></tr></table></figure>
<h1 id="提取Reads,转fasta"><a href="#提取Reads,转fasta" class="headerlink" title="提取Reads,转fasta"></a>提取Reads,转fasta</h1><figure class="highlight plaintext"><table><tr><td class="code"><pre><span class="line">sambamba view -F "ref_name=='******' and not secondary_alignment and not supplementary" ******.bam | cut -f 1,10 | sed 's/^/>/' | sed -r 's/\t/\n/' > Target.fa</span><br></pre></td></tr></table></figure>
]]></content>
<categories>
<category>Log</category>
</categories>
<tags>
<tag>Bam</tag>
<tag>Sambamba</tag>
<tag>Linux</tag>
</tags>
</entry>
<entry>
<title>Cutadapt拆分MGI数据</title>
<url>/2023/05/27/Cutadapt%E6%8B%86%E5%88%86MGI%E6%95%B0%E6%8D%AE/</url>
<content><![CDATA[<p>用Cutadapt拆分MGI测序仪的下机数据</p>
<span id="more"></span>
<h1 id="背景说明"><a href="#背景说明" class="headerlink" title="背景说明"></a>背景说明</h1><p>用华大测序仪上机测序时,如果选择不由测序仪自动拆分,测序完成后,只会得到一个包含index序列的Fastq文件。<br>使用Cutadapt,可以比较方便地按你需要的index,拆分成多个Fastq文件;还可以参数指定用多个线程拆分,会比较快。<br>同样的方法也可以用于一些包含Tag序列的Fastq文件,例如基因表达谱分析(DGE,Digital Gene Expression Tag Profiling)的数据。 </p>
<h1 id="输入文件"><a href="#输入文件" class="headerlink" title="输入文件"></a>输入文件</h1><ul>
<li><p>MGI下机的包含index序列的Fastq文件<br>以下示例是测序读长是50,用的是Dual Barcode 8 bp + 8 bp的Fastq文件。<br><img src="https://pic1.imgdb.cn/item/64719df0f024cca173d96bd8.png" alt="Input_Fq"></p>
</li>
<li><p>目标index序列的Fasta文件<br>按以下格式写成Fasta文件。序列末尾的*$*符号,是为了保证检出的index序列是完整地出现在序列3’末端,详见<a href="https://cutadapt.readthedocs.io/en/stable/guide.html#overview-of-adapter-types">Cutadapt文档 Overview of adapter types</a>。<br><img src="https://pic1.imgdb.cn/item/64719df0f024cca173d96bff.png" alt="Index_Fa"></p>
</li>
</ul>
<h1 id="拆分脚本"><a href="#拆分脚本" class="headerlink" title="拆分脚本"></a>拆分脚本</h1><figure class="highlight plaintext"><table><tr><td class="code"><pre><span class="line"># Shell</span><br><span class="line"></span><br><span class="line">### 参数 ###</span><br><span class="line"># 输入Fastq文件</span><br><span class="line">Input="xxxxxx.fq.gz"</span><br><span class="line"># Index Fasta文件</span><br><span class="line">Index="index.fa"</span><br><span class="line"># 输出目录</span><br><span class="line">Result_Dir="Result"</span><br><span class="line"># 测序读长</span><br><span class="line">Read_Length=50</span><br><span class="line"># 调用核数量</span><br><span class="line">Core=6</span><br><span class="line"></span><br><span class="line">### 拆分 ###</span><br><span class="line">rm -fr $Result_Dir</span><br><span class="line">mkdir -p $Result_Dir</span><br><span class="line"># 用{name}可以使输出文件名用$Index中的Reads ID作为文件名前缀</span><br><span class="line">cutadapt -j $Core --no-indels -e 0 --quality-cutoff 0 --minimum-length $Read_Length --maximum-length $Read_Length -a file:$Index -o $Result_Dir/{name}.fq.gz $Input</span><br><span class="line"></span><br></pre></td></tr></table></figure>
<h1 id="参考资料"><a href="#参考资料" class="headerlink" title="参考资料"></a>参考资料</h1><p><a href="https://cutadapt.readthedocs.io/en/stable/guide.html#demultiplexing">Cutadapt文档 Demultiplexing</a></p>
]]></content>
<categories>
<category>Log</category>
</categories>
<tags>
<tag>Cutadapt</tag>
<tag>MGI</tag>
<tag>数据拆分</tag>
</tags>
</entry>
<entry>
<title>Docker Windows桌面端 释放占用空间</title>
<url>/2023/11/05/Docker-Windows%E6%A1%8C%E9%9D%A2%E7%AB%AF-%E9%87%8A%E6%94%BE%E5%8D%A0%E7%94%A8%E7%A9%BA%E9%97%B4/</url>
<content><![CDATA[<p>Docker Windows桌面端,删除容器后,占用空间没有释放</p>
<span id="more"></span>
<h1 id="问题"><a href="#问题" class="headerlink" title="问题"></a>问题</h1><p>Docker Windows桌面端,删除容器后,占用空间没有释放</p>
<h1 id="原因"><a href="#原因" class="headerlink" title="原因"></a>原因</h1><p>ext4.vhdx磁盘空间会根据加载的数据自动增长,但是无法自动回收。</p>
<h1 id="解决"><a href="#解决" class="headerlink" title="解决"></a>解决</h1><p>注:Docker的ext4.vhdx可能在以下路径:C:\Users\YOURNAME\AppData\Local\Docker\wsl\data </p>
<ol>
<li>退出Docker Windows桌面端 </li>
<li>PowerShell运行:wsl –shutdown </li>
<li>【可选用diskpart】<figure class="highlight plaintext"><table><tr><td class="code"><pre><span class="line"># PowerShell运行以下命令</span><br><span class="line"># 进入diskpart</span><br><span class="line">diskpart</span><br><span class="line"># 选择虚拟机文件</span><br><span class="line">select vdisk file="【填写ext4.vhdx绝对路径】"</span><br><span class="line">attach vdisk readonly</span><br><span class="line"># 回收虚拟机文件无用空间</span><br><span class="line">compact vdisk</span><br><span class="line"># 断开虚拟机文件</span><br><span class="line">detach vdisk</span><br><span class="line"># 退出diskpart</span><br><span class="line">exit</span><br></pre></td></tr></table></figure>
【可选用optimize-vhd,需要已安装Hyper-V】 <figure class="highlight plaintext"><table><tr><td class="code"><pre><span class="line"># PowerShell运行以下命令</span><br><span class="line">optimize-vhd -Path 【填写ext4.vhdx绝对路径】 -Mode full</span><br></pre></td></tr></table></figure></li>
</ol>
<h1 id="参考"><a href="#参考" class="headerlink" title="参考"></a>参考</h1><p>diskpart</p>
<ol>
<li><a href="https://zhuanlan.zhihu.com/p/437983382">https://zhuanlan.zhihu.com/p/437983382</a></li>
<li><a href="https://blog.csdn.net/Caoyang_He/article/details/120507716">https://blog.csdn.net/Caoyang_He/article/details/120507716</a></li>
</ol>
<p>optimize-vhd</p>
<ol>
<li><a href="https://learn.microsoft.com/zh-hk/powershell/module/hyper-v/optimize-vhd?view=windowsserver2022-ps&viewFallbackFrom=win10-ps">https://learn.microsoft.com/zh-hk/powershell/module/hyper-v/optimize-vhd?view=windowsserver2022-ps&viewFallbackFrom=win10-ps</a></li>
<li><a href="https://www.cnblogs.com/cccy0/p/16918476.html">https://www.cnblogs.com/cccy0/p/16918476.html</a></li>
<li><a href="https://www.hanselman.com/blog/shrink-your-wsl2-virtual-disks-and-docker-images-and-reclaim-disk-space">https://www.hanselman.com/blog/shrink-your-wsl2-virtual-disks-and-docker-images-and-reclaim-disk-space</a></li>
<li><a href="https://zhuanlan.zhihu.com/p/538805830">https://zhuanlan.zhihu.com/p/538805830</a></li>
</ol>
]]></content>
<categories>
<category>Log</category>
</categories>
<tags>
<tag>Docker</tag>
</tags>
</entry>
<entry>
<title>Docker转Singularity</title>
<url>/2023/04/24/Docker%E8%BD%ACSingularity/</url>
<content><![CDATA[<p>Docker镜像转换为Singularity的sif格式镜像文件</p>
<span id="more"></span>
<h1 id="需求"><a href="#需求" class="headerlink" title="需求"></a>需求</h1><p>本地搭建了一些docker镜像,已有的方案用Cromwell投递WDL项目时用的是Singularity镜像,所以需要转为Singularity的sif格式镜像文件。 </p>
<h1 id="错误方案"><a href="#错误方案" class="headerlink" title="错误方案"></a>错误方案</h1><p>同事之前已经写了一个将docker hub的镜像pull下来并转为sif格式的脚本,想改成用singularity build去处理本地docker镜像。<br>但是发现生成的sif文件名称没有sha256后面的验证码。<br>正常生成的sif名称类似:***_varscan2_sha256_b235818***************595db587df.sif,但是singularity build生成的的会类似***<em>varscan2_sha256</em>.sif。<br>原因是sha256验证码取的是docker镜像的RepoDigests,此信息只有当镜像被上传到docker hub后才会有。<br>本地搭建的,未上传到docker hub的镜像,使用docker images –digests查看会见到该镜像的DIGEST列的值为<none>。所以其实是sha256码本身就不存在,所以无法生成对应的文件名。<br>其实没有sha256的Singularity的sif格式镜像文件也可以用于Cromwell投递WDL项目,需要Cromwell配置文件设置参数。[这里挖一个坑,写好填上] </p>
<p>已有的用于Docker转换为Singularity的脚本: </p>
<figure class="highlight plaintext"><table><tr><td class="code"><pre><span class="line">#! /bin/bash</span><br><span class="line"></span><br><span class="line">docker=$1</span><br><span class="line"></span><br><span class="line">export SINGULARITY_CACHEDIR=[存放Singularity镜像的目录]</span><br><span class="line">CACHE_DIR=$SINGULARITY_CACHEDIR</span><br><span class="line">DOCKER_NAME=$(echo $docker | cut -d":" -f 1 | sed -e 's/\//_/')</span><br><span class="line">SHA_NAME=$(docker inspect --format='{{index .RepoDigests 0}}' ${docker} | cut -d":" -f 2)</span><br><span class="line">SHA_TAG="sha256_${SHA_NAME}"</span><br><span class="line">IMAGE=$CACHE_DIR/${DOCKER_NAME}_${SHA_TAG}.sif</span><br><span class="line">if [ ! -f $IMAGE ]; then</span><br><span class="line"> singularity pull $IMAGE docker://${docker}</span><br><span class="line">fi</span><br></pre></td></tr></table></figure>
<h1 id="正确方案"><a href="#正确方案" class="headerlink" title="正确方案"></a>正确方案</h1><p>先将本地的docker image上传到docker hub上(<a href="https://blog.csdn.net/u013258415/article/details/80050956/">参考</a>),生成Docker镜像的RepoDigests后,再跑一下上面的shell脚本。 </p>
<ol>
<li>注册docker hub账户,<code>https://hub.docker.com/</code>。 </li>
<li>在服务器上登录docker hub,命令行docker login,输账号密码。 </li>
<li>检查镜像的REPOSITORY命名方式,必须是“注册用户名/镜像名”。不符合的可以用docker tag <old_REPOSITORY> <new_REPOSITORY>修改。修改后可以docker rmi 把旧的删掉。 </new_REPOSITORY></old_REPOSITORY></li>
<li>上传镜像到docker hub,命令行docker push REPOSITORY:TAG,等待上传完毕即可。无需重新pull镜像,上传完本地的镜像就会有RepoDigests,可以通过docker images –digests查看。 </li>
<li>退出当前docker hub账号,命令行docker logout。 </li>
<li>使用上面的shell脚本将docker容器转为sif格式,传入参数是docker image的REPOSITORY:TAG。</li>
</ol>
]]></content>
<categories>
<category>Log</category>
</categories>
<tags>
<tag>Docker</tag>
<tag>Singularity</tag>
<tag>WDL</tag>
<tag>Cromwell</tag>
</tags>
</entry>
<entry>
<title>Falco测试</title>
<url>/2023/12/03/Falco%E6%B5%8B%E8%AF%95/</url>
<content><![CDATA[<p>Falco软件测试,主要看与FastQC的分析时间、结果一致性、报告界面的差异。</p>
<span id="more"></span>
<h1 id="软件版本"><a href="#软件版本" class="headerlink" title="软件版本"></a>软件版本</h1><ul>
<li>falco 1.2.1</li>
<li>FastQC v0.11.8</li>
</ul>
<h1 id="软件简介"><a href="#软件简介" class="headerlink" title="软件简介"></a>软件简介</h1><p><a href="https://github.com/smithlabcode/falco">Falco</a>是对FastQC的emulation(仿真?),基本上是把FastQC重新实现了一遍,应该是用的C++?<br>然后它比FastQC多了些参数,说明文档里有写[Falco only]的例如-subsample、-bisulfite、-reverse-complement等。</p>
<h1 id="测试结果"><a href="#测试结果" class="headerlink" title="测试结果"></a>测试结果</h1><ul>
<li>用一对Fastq文件做了测试,每个Fastq是53692232条序列,读长150。</li>
<li>两个软件的统计结果是一样的。但是Falco的分析时间没有减少很多。考虑到FastQC本身有大部分模块是只抽前100,000条序列计算,计算量不大,时间相差不多也可以理解。<br><img src="https://pic.imgdb.cn/item/656c3886c458853aef95e9ce.png" alt="分析时间比较"></li>
<li>主要问题是,它的html报告需要加载一些在线资源(应该是css还有plotly?),然后动态生成报告和图。但是这些资源在国内访问不了或者加载速度很慢,就变成没图,甚至连报告打不开;但是用了魔法就没问题了。</li>
<li>22年5月的一个Issue有提到这个问题,<a href="https://github.com/smithlabcode/falco/issues/33">add CSS and javascript to HTML page source code</a>,但是没人回复。<br>能打开的时候是这样的,好处是鼠标放图上,能显示具体的值。<br><img src="https://pic.imgdb.cn/item/656c38edc458853aef974722.png" alt="Falco报告界面"></li>
</ul>
<h1 id="测试代码"><a href="#测试代码" class="headerlink" title="测试代码"></a>测试代码</h1><figure class="highlight plaintext"><table><tr><td class="code"><pre><span class="line"># shell</span><br><span class="line"></span><br><span class="line">Test_Dir="/xxx/Software_Test/Falco_QC"</span><br><span class="line">Falco_Result_Dir="$Test_Dir/Result_Falco"</span><br><span class="line">FastQC_Result_Dir="$Test_Dir/Result_FastQC"</span><br><span class="line"></span><br><span class="line">Data_R1="Sample_R1.fastq.gz"</span><br><span class="line">Data_R2="Sample_R2.fastq.gz"</span><br><span class="line"></span><br><span class="line">rm -fr $Falco_Result_Dir $FastQC_Result_Dir</span><br><span class="line">mkdir $Falco_Result_Dir $FastQC_Result_Dir</span><br><span class="line"></span><br><span class="line">echo "[Falco] Start : `date`"</span><br><span class="line">time /xxx/Software/falco/bin/falco --quiet --extract --nogroup --threads 4 -o $Falco_Result_Dir $Data_R1 $Data_R2</span><br><span class="line">echo "[Falco] Finish : `date`"</span><br><span class="line"></span><br><span class="line">echo "-----------------------------------------------------------------------------------------------"</span><br><span class="line"></span><br><span class="line">echo "[FastQC] Start : `date`"</span><br><span class="line">time /xxx/fastqc --quiet --extract --nogroup --threads 4 -o $FastQC_Result_Dir $Data_R1 $Data_R2</span><br><span class="line">echo "[FastQC] Finish : `date`"</span><br></pre></td></tr></table></figure>
<h1 id="结论"><a href="#结论" class="headerlink" title="结论"></a>结论</h1><p>这个软件在国内是个鸡肋:分析时间没减少很多,报告还打不开。<br>除非是有在线云平台想给客户一个有交互的报告界面。但是也要先把那些资源本地化,再修改html文件。还不如自己直接实现一个类似的界面。</p>
]]></content>
<categories>
<category>Log</category>
</categories>
<tags>
<tag>Falco</tag>
<tag>FastQC</tag>
<tag>质控</tag>
</tags>
</entry>
<entry>
<title>Fastq、Fasta文件操作</title>
<url>/2023/05/22/Fastq%E3%80%81Fasta%E6%96%87%E4%BB%B6%E6%93%8D%E4%BD%9C/</url>
<content><![CDATA[<p>用Linux命令行或软件对Fastq、Fasta文件进行操作</p>
<span id="more"></span>
<h1 id="fastq转换为fasta"><a href="#fastq转换为fasta" class="headerlink" title="fastq转换为fasta"></a>fastq转换为fasta</h1><figure class="highlight plaintext"><table><tr><td class="code"><pre><span class="line">awk '{if(NR%4 == 1){print ">" substr($0, 2)}}{if(NR%4 == 2){print}}' $fastq > $fasta</span><br></pre></td></tr></table></figure>
<h1 id="fasta去重"><a href="#fasta去重" class="headerlink" title="fasta去重"></a>fasta去重</h1><figure class="highlight plaintext"><table><tr><td class="code"><pre><span class="line">fastx_toolkit_0.0.13/bin/fastx_collapser -i Target.fa -o Target.dedup.fa</span><br></pre></td></tr></table></figure>
<h1 id="fastq提取并统计某个部分碱基序列"><a href="#fastq提取并统计某个部分碱基序列" class="headerlink" title="fastq提取并统计某个部分碱基序列"></a>fastq提取并统计某个部分碱基序列</h1><figure class="highlight plaintext"><table><tr><td class="code"><pre><span class="line"># 这里举例的是第101个碱基~最后一个碱基</span><br><span class="line">less $fastq | sed -n '0~2p' | sed -n '1~2p' | cut -c 101- | sort | uniq -c | sed -r 's/^\s+//' | sed 's/\s/\t/' > $stat_tsv</span><br></pre></td></tr></table></figure>
]]></content>
<tags>
<tag>Linux</tag>
<tag>Fastq</tag>
<tag>Fasta</tag>
<tag>fastx_toolkit</tag>
</tags>
</entry>
<entry>
<title>GRC patch解释</title>
<url>/2025/04/09/GRC-patch%E8%A7%A3%E9%87%8A/</url>
<content><![CDATA[<p>NBCI BLAST可能会出现序列名称带有“PATCHES XXX”,例如“Homo sapiens chromosome 1 genomic patch of type NOVEL, GRCh38.p14 PATCHES HSCHR1_12_CTG3”。UCSC In-Silico PCR会出现类似“chr1_jh636052_fix”的序列名称。</p>
<span id="more"></span>
<h1 id="NCBI解释"><a href="#NCBI解释" class="headerlink" title="NCBI解释"></a>NCBI解释</h1><p><a href="https://www.ncbi.nlm.nih.gov/grc/help/patches/">Introduction to Patches - Genome Reference Consortium (nih.gov)</a></p>
<h2 id="FIX-patches"><a href="#FIX-patches" class="headerlink" title="FIX patches"></a>FIX patches</h2><p>Fix patches represent changes to existing assembly sequences. These are generally error corrections (addressed by approaches such as base changes, component replacements/updates, switch point updates or tiling path changes) or assembly improvements, such as the extension of sequence into gaps. A fix patch scaffold represents a preview of what the assembly will look like at the next major (coordinate changing) release. When the next major release occurs, the accessions for the fix patch scaffolds will be deprecated and the changes will be found in the chromosomes. </p>
<h2 id="NOVEL-patches"><a href="#NOVEL-patches" class="headerlink" title="NOVEL patches"></a>NOVEL patches</h2><p>Novel patches represent the addition of new alternate loci to the assembly. These are alternate sequence representations of sequence found on the chromosomes. When the next major release occurs, the accessions for the novel patch scaffolds will persist, and the scaffolds will be known as alternate loci. At that time, the scaffolds will move from the PATCHES assembly unit to the relevant alternate loci assembly unit. </p>
<h1 id="UCSC解释"><a href="#UCSC解释" class="headerlink" title="UCSC解释"></a>UCSC解释</h1><p><a href="https://genome-euro.ucsc.edu/cgi-bin/hgc?hgsid=288501639_qiVujGucScr6PP2A0uSsy4QqAfaW&db=hg19&c=chr1&l=142600000&r=147000000&o=145592292&t=145833117&g=fixSeqLiftOverPsl&i=chr1_jh636052_fix">hg19 Human: Reference Assembly Fix Patch Sequence Alignments (chr1_jh636052_fix) (ucsc.edu)</a><br>This track shows alignments of fix patch sequences to main chromosome sequences in the reference genome assembly. When errors are corrected in the reference genome assembly, the Genome Reference Consortium (GRC) adds fix patch sequences containing the corrected regions. This strikes a balance between providing the most complete and correct genome sequence, while maintaining stable chromosome coordinates for the original assembly sequences.<br>Fix patches are often associated with incident reports displayed in the GRC Incidents track. </p>
<h1 id="DeepSeek-R1解释"><a href="#DeepSeek-R1解释" class="headerlink" title="DeepSeek-R1解释"></a>DeepSeek-R1解释</h1><p><strong>Genome Reference Consortium (GRC) 的 Patches 详解</strong><br>GRC 负责维护和更新参考基因组(如人类基因组),以反映科学界对基因组结构的最新理解。由于技术进步或新发现,参考基因组需要定期修正和补充。为此,GRC 引入了两种类型的补丁(Patches):<strong>FIX patches</strong> 和 <strong>NOVEL patches</strong>。以下是它们的详细解释: </p>
<hr>
<h2 id="1-FIX-Patches(修正补丁)"><a href="#1-FIX-Patches(修正补丁)" class="headerlink" title="1. FIX Patches(修正补丁)"></a><strong>1. FIX Patches(修正补丁)</strong></h2><p><strong>定义与作用</strong> </p>
<ul>
<li>FIX patches 是对现有染色体序列的直接<strong>修正或改进</strong>,目的是修复错误或填补已知缺口。 </li>
<li>修正类型包括: <ul>
<li><strong>碱基错误纠正</strong>(如测序错误的单碱基修改)。 </li>
<li><strong>组件替换/更新</strong>(替换不准确的序列片段)。 </li>
<li><strong>路径调整</strong>(优化序列的拼接方式)。 </li>
<li><strong>填补缺口</strong>(通过新数据延伸原有序列,减少未测序区域)。</li>
</ul>
</li>
</ul>
<p><strong>特点与生命周期</strong> </p>
<ul>
<li>FIX patches 以独立支架(scaffold)形式发布,作为<strong>临时预览</strong>,展示下次主版本(major release)的预期变更。 </li>
<li><strong>主版本发布后</strong>: <ul>
<li>FIX patches 的变更会整合到染色体主序列中,其原始 accession 编号(如 <code>KI270752.1</code>)会被弃用。 </li>
<li>用户需切换到新版染色体坐标,旧补丁不再独立存在。</li>
</ul>
</li>
</ul>
<p><strong>示例</strong><br>若原染色体 2 号某区域存在缺口,FIX patch 可能新增一段序列填补该缺口。下次主版本中,这段序列将直接合并到染色体 2,原补丁编号失效。</p>
<hr>
<h2 id="2-NOVEL-Patches(新异源补丁)"><a href="#2-NOVEL-Patches(新异源补丁)" class="headerlink" title="2. NOVEL Patches(新异源补丁)"></a><strong>2. NOVEL Patches(新异源补丁)</strong></h2><p><strong>定义与作用</strong> </p>
<ul>
<li>NOVEL patches 代表染色体某些区域的<strong>替代序列</strong>(alternate loci),反映群体中的遗传多样性或复杂区域的不同单倍型。 </li>
<li>例如:人类主要组织相容性复合体(MHC)区域高度多态,NOVEL patches 可提供不同单倍型的序列版本。</li>
</ul>
<p><strong>特点与生命周期</strong> </p>
<ul>
<li>NOVEL patches 以独立支架形式发布,但<strong>不会整合到主染色体</strong>中,而是作为替代位点保留。 </li>
<li><strong>主版本发布后</strong>: <ul>
<li>其 accession 编号(如 <code>KI270757.1</code>)会保留,但分类从“补丁”调整为“替代位点”(alternate loci)。 </li>
<li>移至专门的“替代位点集合”(如 <code>ALT_REF_LOCI_1</code>),供研究者按需使用。</li>
</ul>
</li>
</ul>
<p><strong>示例</strong><br>若染色体 17 号某区域存在两种常见结构变异,NOVEL patch 可为每种变异提供独立序列。主版本发布后,这些序列作为替代位点与主染色体并存。</p>
<hr>
<h2 id="核心区别"><a href="#核心区别" class="headerlink" title="核心区别"></a><strong>核心区别</strong></h2><table>
<thead>
<tr>
<th>特征</th>
<th>FIX Patches</th>
<th>NOVEL Patches</th>
</tr>
</thead>
<tbody><tr>
<td><strong>目的</strong></td>
<td>修正错误、填补缺口</td>
<td>提供替代序列(遗传多样性)</td>
</tr>
<tr>
<td><strong>主版本后状态</strong></td>
<td>整合到染色体,原编号失效</td>
<td>保留为替代位点,编号不变</td>
</tr>
<tr>
<td><strong>数据归属</strong></td>
<td>最终归属主序列</td>
<td>长期独立存在,补充主序列</td>
</tr>
</tbody></table>
<hr>
<h2 id="为何需要-Patches?"><a href="#为何需要-Patches?" class="headerlink" title="为何需要 Patches?"></a><strong>为何需要 Patches?</strong></h2><ul>
<li><strong>持续改进</strong>:在不破坏现有坐标系统的前提下(非主版本期间),及时修正错误或添加新数据。 </li>
<li><strong>兼容性</strong>:研究者可提前预览变更,同时保持旧版本数据的稳定性。 </li>
<li><strong>多样性管理</strong>:通过替代位点支持复杂区域的遗传变异研究(如免疫相关基因)。</li>
</ul>
<hr>
<h2 id="总结"><a href="#总结" class="headerlink" title="总结"></a><strong>总结</strong></h2><p>FIX 和 NOVEL patches 是 GRC 维护参考基因组的核心工具,前者确保准确性,后者反映多样性。两者协同工作,使参考基因组成为动态更新的资源,既稳定又适应科学进步。用户需注意主版本更新时的数据迁移规则,以正确引用最新或替代序列。</p>
<h1 id="总结-1"><a href="#总结-1" class="headerlink" title="总结"></a>总结</h1><p>GRC会不定期以major或minor的形式对参考基因组进行更新。major表示基因组原序列碱基或坐标有相对较大的改动,会提供新的编号,如GRCh37、GRCh38等;minor则是patch的形式,如GRCh38.p13等,其基因组原序列无变动,主要是新增了fix patch和noval patch两种,其中fix patch是对原基因组序列的更新和修正,其内容会在下一次major中并入,noval patch则是新的单倍体型。<a href="https://wenlongshen.github.io/2020/03/26/Reference-Genome/">关于人类基因组的一些说明</a> </p>
]]></content>
<categories>
<category>Log</category>
</categories>
<tags>
<tag>BLAST</tag>
<tag>In-Silico PCR</tag>
</tags>
</entry>
<entry>
<title>Hexo常用命令</title>
<url>/2025/03/25/Hexo%E5%B8%B8%E7%94%A8%E5%91%BD%E4%BB%A4/</url>
<content><![CDATA[<p>Hexo搭建博客常用的命令</p>
<span id="more"></span>
<h1 id="参考文章"><a href="#参考文章" class="headerlink" title="参考文章"></a>参考文章</h1><p>以下第1.2.步可以参考以下一些文章,会更详细清晰<br><a href="https://blog.csdn.net/itcast_cn/article/details/129876490">Hexo+github搭建个人博客网站</a><br><a href="https://blog.csdn.net/lang_xw/article/details/143050877">GitHub+Hexo搭建个人博客 - 详细教程</a><br><a href="https://zhuanlan.zhihu.com/p/688561305">【2024】从零开始用Hexo+GithubPage搭建个人网站(保姆级)</a> </p>
<h1 id="1-部署GitHub仓库-x2F-Pages"><a href="#1-部署GitHub仓库-x2F-Pages" class="headerlink" title="1. 部署GitHub仓库/Pages"></a>1. 部署GitHub仓库/Pages</h1><ol>
<li>注册 GitHub 账号 </li>
<li>在 GitHub 创建仓库,命名为 <code><username>.github.io</code>(个人主页)或自定义仓库。 </li>
<li>安装 Hexo 部署插件 <figure class="highlight bash"><table><tr><td class="code"><pre><span class="line">npm install hexo-deployer-git --save</span><br></pre></td></tr></table></figure></li>
<li>修改 Hexo 的 <code>_config.yml</code>,添加部署配置 <figure class="highlight yml"><table><tr><td class="code"><pre><span class="line"><span class="attr">deploy:</span></span><br><span class="line"> <span class="attr">type:</span> <span class="string">git</span></span><br><span class="line"> <span class="attr">repo:</span> <span class="string">https://github.com/<username>/<repository>.git</span></span><br><span class="line"> <span class="attr">branch:</span> <span class="string">main</span> <span class="comment"># 或 gh-pages(自定义仓库时常用)</span></span><br></pre></td></tr></table></figure></li>
</ol>
<h1 id="2-Hexo环境"><a href="#2-Hexo环境" class="headerlink" title="2. Hexo环境"></a>2. Hexo环境</h1><figure class="highlight bash"><table><tr><td class="code"><pre><span class="line"><span class="comment"># 安装 Hexo 命令行工具</span></span><br><span class="line">npm install -g hexo-cli</span><br><span class="line"></span><br><span class="line"><span class="comment"># 初始化 Hexo 项目(替换 <folder> 为你的项目目录名)</span></span><br><span class="line">hexo init <folder></span><br><span class="line"><span class="built_in">cd</span> <folder></span><br></pre></td></tr></table></figure>
<h1 id="3-编写博客"><a href="#3-编写博客" class="headerlink" title="3. 编写博客"></a>3. 编写博客</h1><p><a href="https://hexo.io/zh-cn/">Hexo官网</a><br><a href="https://hexo.io/themes/">Hexo主题</a> </p>
<figure class="highlight bash"><table><tr><td class="code"><pre><span class="line"><span class="comment"># 创建新文章(在 source/_posts 下生成 Markdown 文件,生成后会提示绝对路径)</span></span><br><span class="line"><span class="comment"># source/scaffolds/post.md 是文章模板,hexo new会基于此模板生成Markdown 文件,可以根据需要自定义模板</span></span><br><span class="line">hexo new <span class="string">"文章标题"</span></span><br><span class="line"></span><br><span class="line"><span class="comment"># 启动本地服务器(默认 http://localhost:4000),可在浏览器实时预览博客效果</span></span><br><span class="line">hexo server <span class="comment"># 可以简写: hexo s</span></span><br></pre></td></tr></table></figure>
<h1 id="4-部署到GitHub"><a href="#4-部署到GitHub" class="headerlink" title="4. 部署到GitHub"></a>4. 部署到GitHub</h1><figure class="highlight bash"><table><tr><td class="code"><pre><span class="line"><span class="comment"># 组合命令:清除缓存和旧生成文件 + 生成 + 部署</span></span><br><span class="line">hexo clean; hexo generate; hexo deploy </span><br></pre></td></tr></table></figure>
]]></content>
<categories>
<category>Log</category>
</categories>
<tags>
<tag>Hexo</tag>
<tag>GitHub</tag>
<tag>Blog</tag>
</tags>
</entry>
<entry>
<title>IGV自定义参考基因组</title>
<url>/2023/05/03/IGV%E8%87%AA%E5%AE%9A%E4%B9%89%E5%8F%82%E8%80%83%E5%9F%BA%E5%9B%A0%E7%BB%84/</url>
<content><![CDATA[<p>IGV 2.11.0版本以上,自定义参考基因组的方法</p>
<span id="more"></span>
<h1 id="软件版本"><a href="#软件版本" class="headerlink" title="软件版本"></a>软件版本</h1><p>IGV版本:2.13.0 </p>
<h1 id="需求说明"><a href="#需求说明" class="headerlink" title="需求说明"></a>需求说明</h1><p>对b37的参考基因组fasta文件做了一些修改,需要在IGV中浏览它,而且需要有Refseq的基因注释信息的Track。 </p>
<h1 id="信息说明"><a href="#信息说明" class="headerlink" title="信息说明"></a>信息说明</h1><h2 id="版本差异"><a href="#版本差异" class="headerlink" title="版本差异"></a>版本差异</h2><p>IGV 2.11.0版本以上,是用一个JSON文件去指定和加载参考基因组的。<br>同时弃用了之前版本的.genome格式;通过选项Genomes -> Greate .genome File…的加载方式也取消了。 </p>
<h2 id="官方文档"><a href="#官方文档" class="headerlink" title="官方文档"></a>官方文档</h2><p><a href="https://github.com/igvteam/igv/wiki/JSON-Genome-Format">格式说明</a> <code>https://github.com/igvteam/igv/wiki/JSON-Genome-Format</code><br><a href="https://github.com/igvteam/igv.js/wiki/Reference-Genome">属性说明</a> <code>https://github.com/igvteam/igv.js/wiki/Reference-Genome</code> </p>
<h2 id="参数说明"><a href="#参数说明" class="headerlink" title="参数说明"></a>参数说明</h2><p>IGV 2.11.0版本以上自定义参考基因组JSON文件,只有是fastaURL必填,其他都是可选。<br>所有URL都可以是在线资源或本地路径。 </p>
<ul>
<li>id:该参考基因组的名称,可选。 <del>就是在Genome下拉框里显示的基因组名称。</del> 如果需要使用BLAT功能的话,这里要填某些特定的genome ID。具体原因见<code>IGV的BLAT</code>。 </li>
<li>name:描述信息,可选。就是在Genome下拉框里显示的基因组名称。 </li>
<li>fastaURL:参考基因组Fasta的URL,必填。可以是线上的,如UCSC等数据库中的fasta文件;也可以是本地的,如服务器上的fasta文件路径。 </li>
<li>indexURL:参考基因组Fasta的索引(.fai)文件,可选。但如果不提供.fai文件,会一次性加载整个fasta文件。 </li>
<li>cytobandURL:UCSC格式的cytoBand文件的URL,可选。是用于画染色体示意图的,可以在UCSC的goldenPath找到cytoBand.txt.gz,例如<a href="https://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/">hg19</a>的。UCSC上有<a href="https://genome.ucsc.edu/cgi-bin/hgTables?db=hg38&hgta_group=map&hgta_track=cytoBand&hgta_table=cytoBand&hgta_doSchema=describe+table+schema">cytoBand文件格式说明</a>。 </li>
<li>tracks:加载参考基因组时,同时加载的一系列Tracks,例如默认的hg19基因组的RefSeq Gene描述信息,可选。IGV的Github有<a href="https://github.com/igvteam/igv.js/wiki/Tracks-2.0">tracks格式说明</a>。</li>
</ul>
<h2 id="加载方法"><a href="#加载方法" class="headerlink" title="加载方法"></a>加载方法</h2><p>写完JSON文件后,在软件中加载自定义参考基因组的方法:Genomes -> Load Genome from File… -> 选择参考基因组json文件</p>
<h1 id="JSON示例"><a href="#JSON示例" class="headerlink" title="JSON示例"></a>JSON示例</h1><p>示例的详细信息见:<a href="https://igv.org/doc/desktop/#FileFormats/Genomes/#igv-reference-genome-json">IGV reference genome (JSON)</a></p>
<figure class="highlight plaintext"><table><tr><td class="code"><pre><span class="line">{</span><br><span class="line"> "id": "hg38",</span><br><span class="line"> "name": "Human (GRCh38/hg38)",</span><br><span class="line"> "fastaURL": "https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa",</span><br><span class="line"> "indexURL": "https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa.fai",</span><br><span class="line"> "cytobandURL": "https://s3.amazonaws.com/igv.org.genomes/hg38/annotations/cytoBandIdeo.txt.gz",</span><br><span class="line"> "aliasURL": "https://s3.amazonaws.com/igv.org.genomes/hg38/hg38_alias.tab",</span><br><span class="line"> "chromosomeOrder": [</span><br><span class="line"> "chr1",</span><br><span class="line"> "chr2",</span><br><span class="line"> "chr3",</span><br><span class="line"> "chr4",</span><br><span class="line"> "chr5",</span><br><span class="line"> "chr6",</span><br><span class="line"> "chr7",</span><br><span class="line"> "chr8",</span><br><span class="line"> "chr9",</span><br><span class="line"> "chr10",</span><br><span class="line"> "chr11",</span><br><span class="line"> "chr12",</span><br><span class="line"> "chr13",</span><br><span class="line"> "chr14",</span><br><span class="line"> "chr15",</span><br><span class="line"> "chr16",</span><br><span class="line"> "chr17",</span><br><span class="line"> "chr18",</span><br><span class="line"> "chr19",</span><br><span class="line"> "chr20",</span><br><span class="line"> "chr21",</span><br><span class="line"> "chr22",</span><br><span class="line"> "chrX",</span><br><span class="line"> "chrY"</span><br><span class="line"> ],</span><br><span class="line"> "tracks": [</span><br><span class="line"> {</span><br><span class="line"> "name": "Refseq Genes",</span><br><span class="line"> "format": "refgene",</span><br><span class="line"> "url": "https://s3.amazonaws.com/igv.org.genomes/hg38/ncbiRefSeq.sorted.txt.gz",</span><br><span class="line"> "indexURL": "https://s3.amazonaws.com/igv.org.genomes/hg38/ncbiRefSeq.sorted.txt.gz.tbi"</span><br><span class="line"> },</span><br><span class="line"> {</span><br><span class="line"> "name": "Gencode v24 genes",</span><br><span class="line"> "format": "gtf",</span><br><span class="line"> "url": "https://s3.amazonaws.com/igv.org.genomes/hg19/gencode.v24.genes.gtf.gz"</span><br><span class="line"> }</span><br><span class="line"> ]</span><br><span class="line">}</span><br></pre></td></tr></table></figure>
<h1 id="IGV的BLAT"><a href="#IGV的BLAT" class="headerlink" title="IGV的BLAT"></a>IGV的BLAT</h1><p><a href="https://igv.org/doc/desktop/#UserGuide/tools/blat/">BLAT</a><br><a href="https://igv.org/doc/desktop/#UserGuide/reference_genome/">Reference genome</a><br>从以上官方文档可以知道,IGV的BLAT功能,本质是将待查询序列形成一个命令,传到UCSC的网页服务进行分析。<br>所以如果命令中的某些参数不对,会导致BLAT功能失效,例如指定数据库的db参数。经过测试发现JSON文件的id就是命令中的db参数。<br>从<a href="https://igv.org/doc/desktop/#UserGuide/reference_genome/">Reference genome</a>的<code>Hosting genomes</code>这部分有个<code>https://igv.org/genomes/genomes.tsv</code>,在里面可以看到IGV自带的各个基因组的JSON文件,以及genome ID(db参数/JSON文件的id取值)。 </p>
<ul>
<li>如果你只是想把IGV自带的参考基因组文件下载到本地,避免每次都要等加载;同时要保留BLAT功能。那么JSON文件的id取值必须要是genomes.tsv中的genome ID。</li>
<li>如果你的物种或者参考基因组不是IGV自带的,或者想调用本地服务器的BLAT功能,可以看这篇文章:<a href="https://www.jianshu.com/p/e5aceeb98a98">如何在IGV上使用BLAT搜索非模式物种</a>。</li>
</ul>
<p><code>https://igv.org/genomes/genomes.tsv</code></p>
<table>
<thead>
<tr>
<th align="center">Name (for menu)</th>
<th align="center">url to .genome or .json file</th>
<th align="center">genome ID</th>
</tr>
</thead>
<tbody><tr>
<td align="center">A. thaliana (TAIR 10)</td>
<td align="center"><a href="https://igv.org/genomes/json/tair10.json">https://igv.org/genomes/json/tair10.json</a></td>
<td align="center">tair10</td>
</tr>
<tr>
<td align="center">C. elegans (ce11)</td>
<td align="center"><a href="https://igv.org/genomes/json/ce11.json">https://igv.org/genomes/json/ce11.json</a></td>
<td align="center">ce11</td>
</tr>
<tr>
<td align="center">Chicken (GRCg6a / galGal6)</td>
<td align="center"><a href="https://igv.org/genomes/json/galGal6.json">https://igv.org/genomes/json/galGal6.json</a></td>
<td align="center">galGal6</td>
</tr>
<tr>
<td align="center">Gallus gallus (GCF_016699485.2)</td>
<td align="center"><a href="https://igv.org/genomes/json/GCF_016699485.2/GCF_016699485.2.json">https://igv.org/genomes/json/GCF_016699485.2/GCF_016699485.2.json</a></td>
<td align="center">GCF_016699485.2</td>
</tr>
<tr>
<td align="center">Chimp (panTro4)</td>
<td align="center"><a href="https://igv.org/genomes/json/panTro4.json">https://igv.org/genomes/json/panTro4.json</a></td>
<td align="center">panTro4</td>
</tr>
<tr>
<td align="center">Coprinopsis cinerea okayama7#130 (GCA_000182895.1)</td>
<td align="center"><a href="https://igv.org/genomes/json/GCA_000182895.1/GCA_000182895.1_dt.json">https://igv.org/genomes/json/GCA_000182895.1/GCA_000182895.1_dt.json</a></td>
<td align="center">GCA_000182895.1</td>
</tr>
<tr>
<td align="center">Cow (bosTau8)</td>
<td align="center"><a href="https://igv.org/genomes/json/bosTau8.json">https://igv.org/genomes/json/bosTau8.json</a></td>
<td align="center">bosTau8</td>
</tr>
<tr>
<td align="center">Cow (bosTau9)</td>
<td align="center"><a href="https://igv.org/genomes/json/bosTau9.json">https://igv.org/genomes/json/bosTau9.json</a></td>
<td align="center">bosTau9</td>
</tr>
<tr>
<td align="center">D. melanogaster (dm6)</td>
<td align="center"><a href="https://igv.org/genomes/json/dm6.json">https://igv.org/genomes/json/dm6.json</a></td>
<td align="center">dm6</td>
</tr>
<tr>
<td align="center">D. melanogaster (dm3)</td>
<td align="center"><a href="https://igv.org/genomes/json/dm3.json">https://igv.org/genomes/json/dm3.json</a></td>
<td align="center">dm3</td>
</tr>
<tr>
<td align="center">D. melanogaster (r5.9)</td>
<td align="center"><a href="https://igv.org/genomes/json/dmel_r5.9.json">https://igv.org/genomes/json/dmel_r5.9.json</a></td>
<td align="center">dmel_r5.9</td>
</tr>
<tr>
<td align="center">Dog (canFam3)</td>
<td align="center"><a href="https://igv.org/genomes/json/canFam3.json">https://igv.org/genomes/json/canFam3.json</a></td>
<td align="center">canFam3</td>
</tr>
<tr>
<td align="center">Dog (UU_Cfam_GSD_1.0/canFam4)</td>
<td align="center"><a href="https://igv.org/genomes/json/canFam4.json">https://igv.org/genomes/json/canFam4.json</a></td>
<td align="center">canFam4</td>
</tr>
<tr>
<td align="center">Dog (canFam5)</td>
<td align="center"><a href="https://igv.org/genomes/json/canFam5.json">https://igv.org/genomes/json/canFam5.json</a></td>
<td align="center">canFam5</td>
</tr>
<tr>
<td align="center">Human (1kg, b37+decoy)</td>
<td align="center"><a href="https://igv.org/genomes/json/b37_1kg.json">https://igv.org/genomes/json/b37_1kg.json</a></td>
<td align="center">1kg_v37</td>
</tr>
<tr>
<td align="center">Human (T2T CHM13-v2.0/hs1)</td>
<td align="center"><a href="https://igv.org/genomes/json/hs1.json">https://igv.org/genomes/json/hs1.json</a></td>
<td align="center">hs1</td>
</tr>
<tr>
<td align="center">Human (T2T CHM13-v1.1)</td>
<td align="center"><a href="https://igv.org/genomes/json/chm13v1.1.json">https://igv.org/genomes/json/chm13v1.1.json</a></td>
<td align="center">chm13v1.1</td>
</tr>
<tr>
<td align="center">Human (hg18)</td>
<td align="center"><a href="https://igv.org/genomes/json/hg18.json">https://igv.org/genomes/json/hg18.json</a></td>
<td align="center">hg18</td>
</tr>
<tr>
<td align="center">Human (hg19)</td>
<td align="center"><a href="https://igv.org/genomes/json/hg19.json">https://igv.org/genomes/json/hg19.json</a></td>
<td align="center">hg19</td>
</tr>
<tr>
<td align="center">Human (hg38)</td>
<td align="center"><a href="https://igv.org/genomes/json/hg38.json">https://igv.org/genomes/json/hg38.json</a></td>
<td align="center">hg38</td>
</tr>
<tr>
<td align="center">Human (hg38 1kg/GATK)</td>
<td align="center"><a href="https://igv.org/genomes/json/hg38_1kg.json">https://igv.org/genomes/json/hg38_1kg.json</a></td>
<td align="center">hg38_1kg</td>
</tr>
<tr>
<td align="center">Macaca fascicularis 6.0 (GCA_011100615.1)</td>
<td align="center"><a href="https://igv.org/genomes/json/GCA_011100615.1.json">https://igv.org/genomes/json/GCA_011100615.1.json</a></td>
<td align="center">GCA_011100615.1</td>
</tr>
<tr>
<td align="center">Mouse mm10</td>
<td align="center"><a href="https://igv.org/genomes/json/mm10.json">https://igv.org/genomes/json/mm10.json</a></td>
<td align="center">mm10</td>
</tr>
<tr>
<td align="center">Mouse mm9</td>
<td align="center"><a href="https://igv.org/genomes/json/mm9.json">https://igv.org/genomes/json/mm9.json</a></td>
<td align="center">mm9</td>
</tr>
<tr>
<td align="center">Mouse mm39</td>
<td align="center"><a href="https://igv.org/genomes/json/mm39.json">https://igv.org/genomes/json/mm39.json</a></td>
<td align="center">mm39</td>
</tr>
<tr>
<td align="center">Rat (rn6)</td>
<td align="center"><a href="https://igv.org/genomes/json/rn6.json">https://igv.org/genomes/json/rn6.json</a></td>
<td align="center">rn6</td>
</tr>
<tr>
<td align="center">Rat (rn7)</td>
<td align="center"><a href="https://igv.org/genomes/json/rn7.json">https://igv.org/genomes/json/rn7.json</a></td>
<td align="center">rn7</td>
</tr>
<tr>
<td align="center">S. cerevisiae (sacCer3)</td>
<td align="center"><a href="https://igv.org/genomes/json/sacCer3.json">https://igv.org/genomes/json/sacCer3.json</a></td>
<td align="center">sacCer3</td>
</tr>
<tr>
<td align="center">Zebrafish (GRCz10/danRer10)</td>
<td align="center"><a href="https://igv.org/genomes/json/danRer10.json">https://igv.org/genomes/json/danRer10.json</a></td>
<td align="center">danRer10</td>
</tr>
<tr>
<td align="center">Zebrafish (GRCz11/danRer11)</td>
<td align="center"><a href="https://igv.org/genomes/json/danRer11.json">https://igv.org/genomes/json/danRer11.json</a></td>
<td align="center">danRer11</td>
</tr>
<tr>
<td align="center">SARS-CoV-2</td>
<td align="center"><a href="https://igv.org/genomes/json/ASM985889v3.json">https://igv.org/genomes/json/ASM985889v3.json</a></td>
<td align="center">ASM985889v3</td>
</tr>
<tr>
<td align="center">S. pombe (ASM294v2)</td>
<td align="center"><a href="https://igv.org/genomes/json/ASM294v2.json">https://igv.org/genomes/json/ASM294v2.json</a></td>
<td align="center">ASM294v2</td>
</tr>
<tr>
<td align="center">Gorilla (gorGor4)</td>
<td align="center"><a href="https://igv.org/genomes/json/gorGor4.json">https://igv.org/genomes/json/gorGor4.json</a></td>
<td align="center">gorGor4</td>
</tr>
<tr>
<td align="center">Gorilla (gorGor6)</td>
<td align="center"><a href="https://igv.org/genomes/json/gorGor6.json">https://igv.org/genomes/json/gorGor6.json</a></td>
<td align="center">gorGor6</td>
</tr>
<tr>
<td align="center">Bonobo (MPI-EVA panpan1.1/panPan2)</td>
<td align="center"><a href="https://igv.org/genomes/json/panPan2.json">https://igv.org/genomes/json/panPan2.json</a></td>
<td align="center">panPan2</td>
</tr>
<tr>
<td align="center">Pig (SGSC Sscrofa11.1/susScr11)</td>
<td align="center"><a href="https://igv.org/genomes/json/susScr11.json">https://igv.org/genomes/json/susScr11.json</a></td>
<td align="center">susScr11</td>
</tr>
<tr>
<td align="center">S. purpuratus (Baylor 2.1/strPur2)</td>
<td align="center"><a href="https://igv.org/genomes/json/strPur2.json">https://igv.org/genomes/json/strPur2.json</a></td>
<td align="center">strPur2</td>
</tr>
<tr>
<td align="center">S. purpuratus (Spur5.0)</td>
<td align="center"><a href="https://igv.org/genomes/json/Spur5.0.json">https://igv.org/genomes/json/Spur5.0.json</a></td>
<td align="center">Spur5.0</td>
</tr>
<tr>
<td align="center">P. miniata (Pmin3.0)</td>
<td align="center"><a href="https://igv.org/genomes/json/Pmin3.0.json">https://igv.org/genomes/json/Pmin3.0.json</a></td>
<td align="center">Pmin3.0</td>
</tr>
<tr>
<td align="center">L. variegatus (Lvar3.0)</td>
<td align="center"><a href="https://igv.org/genomes/json/Lvar3.0.json">https://igv.org/genomes/json/Lvar3.0.json</a></td>
<td align="center">Lvar3.0</td>
</tr>
<tr>
<td align="center">O. sativa IRGSP-1.0 (GCF_001433935.1)</td>
<td align="center"><a href="https://igv.org/genomes/json/GCF_001433935.1.json">https://igv.org/genomes/json/GCF_001433935.1.json</a></td>
<td align="center">GCF_001433935.1</td>
</tr>
<tr>
<td align="center">A. gambia (Pest AgamP3)</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/AgamP3.genome">https://s3.amazonaws.com/igv.broadinstitute.org/genomes/AgamP3.genome</a></td>
<td align="center">AgamP3</td>
</tr>
<tr>
<td align="center">Autographa californica MNPV</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/NC_001623.genome">https://s3.amazonaws.com/igv.broadinstitute.org/genomes/NC_001623.genome</a></td>
<td align="center">NC_001623</td>
</tr>
<tr>
<td align="center">Bacillus Subtilis str. 168</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/NC_000964.genome">https://s3.amazonaws.com/igv.broadinstitute.org/genomes/NC_000964.genome</a></td>
<td align="center">NC_000964</td>
</tr>
<tr>
<td align="center">Banana (M. Balbisiana PKWv1)</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/MusaBalbisianaPKWv1.genome">https://s3.amazonaws.com/igv.broadinstitute.org/genomes/MusaBalbisianaPKWv1.genome</a></td>
<td align="center">MusaBalbisianaPKWv1</td>
</tr>
<tr>
<td align="center">Banana (Musa acuminata)</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/MusaAcuminata.genome">https://s3.amazonaws.com/igv.broadinstitute.org/genomes/MusaAcuminata.genome</a></td>
<td align="center">MusaAcuminata</td>
</tr>
<tr>
<td align="center">C. alibcans (SC5314 A21)</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/ca21.genome">https://s3.amazonaws.com/igv.broadinstitute.org/genomes/ca21.genome</a></td>
<td align="center">ca21</td>
</tr>
<tr>
<td align="center">C. elegans (WS241)</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/ws241.genome">https://s3.amazonaws.com/igv.broadinstitute.org/genomes/ws241.genome</a></td>
<td align="center">ws241</td>
</tr>
<tr>
<td align="center">C. elegans (WS235)</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/ws235.genome">https://s3.amazonaws.com/igv.broadinstitute.org/genomes/ws235.genome</a></td>
<td align="center">ws235</td>
</tr>
<tr>
<td align="center">C. elegans (WS245)</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/WS245.genome">https://s3.amazonaws.com/igv.broadinstitute.org/genomes/WS245.genome</a></td>
<td align="center">WS245</td>
</tr>
<tr>
<td align="center">C. elegans (ce10)</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/ce10.genome">https://s3.amazonaws.com/igv.broadinstitute.org/genomes/ce10.genome</a></td>
<td align="center">ce10</td>
</tr>
<tr>
<td align="center">Chicken (galGal4)</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/galGal4.genome">https://s3.amazonaws.com/igv.broadinstitute.org/genomes/galGal4.genome</a></td>
<td align="center">galGal4</td>
</tr>
<tr>
<td align="center">Chicken (galGal5)</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/galGal5.genome">https://s3.amazonaws.com/igv.broadinstitute.org/genomes/galGal5.genome</a></td>
<td align="center">galGal5</td>
</tr>
<tr>
<td align="center">Chimp (panTro3)</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/panTro3.genome">https://s3.amazonaws.com/igv.broadinstitute.org/genomes/panTro3.genome</a></td>
<td align="center">panTro3</td>
</tr>
<tr>
<td align="center">Chimp (panTro5)</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.org.genomes/panTro5/panTro5.genome">https://s3.amazonaws.com/igv.org.genomes/panTro5/panTro5.genome</a></td>
<td align="center">panTro5</td>
</tr>
<tr>
<td align="center">Chimp (panTro6)</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.org.genomes/panTro6/panTro6.genome">https://s3.amazonaws.com/igv.org.genomes/panTro6/panTro6.genome</a></td>
<td align="center">panTro6</td>
</tr>
<tr>
<td align="center">Cat (felCat5)</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/felCat5.genome">https://s3.amazonaws.com/igv.broadinstitute.org/genomes/felCat5.genome</a></td>
<td align="center">felCat5</td>
</tr>
<tr>
<td align="center">Cow (bosTau7)</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/bosTau7.genome">https://s3.amazonaws.com/igv.broadinstitute.org/genomes/bosTau7.genome</a></td>
<td align="center">bosTau7</td>
</tr>
<tr>
<td align="center">E. coli K-12 MG1655 (NC_000913.2)</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/NC_000913.2.genome">https://s3.amazonaws.com/igv.broadinstitute.org/genomes/NC_000913.2.genome</a></td>
<td align="center">NC_000913.2</td>
</tr>
<tr>
<td align="center">E. coli K-12 (NC_000913.3)</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/NC_000913.3.gbk">https://s3.amazonaws.com/igv.broadinstitute.org/genomes/NC_000913.3.gbk</a></td>
<td align="center">NC_000913.3</td>
</tr>
<tr>
<td align="center">Ferret (MusPutFur1.0)</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/MusPutFur1.0.genome">https://s3.amazonaws.com/igv.broadinstitute.org/genomes/MusPutFur1.0.genome</a></td>
<td align="center">MusPutFur1.0</td>
</tr>
<tr>
<td align="center">Francisella tularensis (NC_008601)</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/NC_008601.gbk">https://s3.amazonaws.com/igv.broadinstitute.org/genomes/NC_008601.gbk</a></td>
<td align="center">NC_008601</td>
</tr>
<tr>
<td align="center">Glycine max (v8.0)</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/gmax8.genome">https://s3.amazonaws.com/igv.broadinstitute.org/genomes/gmax8.genome</a></td>
<td align="center">gmax8</td>
</tr>
<tr>
<td align="center">Glycine max (Wm82.a2.v1)</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/gmax10.genome">https://s3.amazonaws.com/igv.broadinstitute.org/genomes/gmax10.genome</a></td>
<td align="center">gmax10</td>
</tr>
<tr>
<td align="center">Helicobacter hepaticus</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/NC_004917.genome">https://s3.amazonaws.com/igv.broadinstitute.org/genomes/NC_004917.genome</a></td>
<td align="center">NC_004917</td>
</tr>
<tr>
<td align="center">HIV-1</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/NC_001802.genome">https://s3.amazonaws.com/igv.broadinstitute.org/genomes/NC_001802.genome</a></td>
<td align="center">NC_001802</td>
</tr>
<tr>
<td align="center">HIV-2</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/NC_001722.genome">https://s3.amazonaws.com/igv.broadinstitute.org/genomes/NC_001722.genome</a></td>
<td align="center">NC_001722</td>
</tr>
<tr>
<td align="center">Human Adenovirus C</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/NC_001405.genome">https://s3.amazonaws.com/igv.broadinstitute.org/genomes/NC_001405.genome</a></td>
<td align="center">NC_001405</td>
</tr>
<tr>
<td align="center">Human Herpesvirus 4, Type 1</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/HHV4_Type1.genome">https://s3.amazonaws.com/igv.broadinstitute.org/genomes/HHV4_Type1.genome</a></td>
<td align="center">HHV4_Type1</td>
</tr>
<tr>
<td align="center">Human Herpesvirus 4, Type 2</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/HHV4_Type2.genome">https://s3.amazonaws.com/igv.broadinstitute.org/genomes/HHV4_Type2.genome</a></td>
<td align="center">HHV4_Type2</td>
</tr>
<tr>
<td align="center">Human Mito (NC_012920)</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/NC_012920.1.gbk">https://s3.amazonaws.com/igv.broadinstitute.org/genomes/NC_012920.1.gbk</a></td>
<td align="center">NC_012920</td>
</tr>
<tr>
<td align="center">Human respiratory synctial virus</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/M74568.genome">https://s3.amazonaws.com/igv.broadinstitute.org/genomes/M74568.genome</a></td>
<td align="center">M74568</td>
</tr>
<tr>
<td align="center">Macaca fascicularis (CE_1.0)</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/CE_1.0.genome">https://s3.amazonaws.com/igv.broadinstitute.org/genomes/CE_1.0.genome</a></td>
<td align="center">CE_1.0</td>
</tr>
<tr>
<td align="center">Macaca fascicularis (5.0)</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.org.genomes/Macaca_fascicularis_5.0/Macaca_fascicularis_5.0.genome">https://s3.amazonaws.com/igv.org.genomes/Macaca_fascicularis_5.0/Macaca_fascicularis_5.0.genome</a></td>
<td align="center">GCF_000364345.1</td>
</tr>
<tr>
<td align="center">Mouse (129S1/SvImJ)</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/SvImJ.genome">https://s3.amazonaws.com/igv.broadinstitute.org/genomes/SvImJ.genome</a></td>
<td align="center">129S1/SvImJ</td>
</tr>
<tr>
<td align="center">Mouse mm8</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/mm8.genome">https://s3.amazonaws.com/igv.broadinstitute.org/genomes/mm8.genome</a></td>
<td align="center">mm8</td>
</tr>
<tr>
<td align="center">Mycobacterium TB (CD1551)</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/NC_002755.genome">https://s3.amazonaws.com/igv.broadinstitute.org/genomes/NC_002755.genome</a></td>
<td align="center">NC_002755</td>
</tr>
<tr>
<td align="center">N. Meningitidis (FAM18)</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.broadinstitute.org/test/genomes/NC_008767.genome">https://s3.amazonaws.com/igv.broadinstitute.org/test/genomes/NC_008767.genome</a></td>
<td align="center">NC_008767</td>
</tr>
<tr>
<td align="center">N. Meningitidis (MC58)</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.broadinstitute.org/test/genomes/NC_003112.genome">https://s3.amazonaws.com/igv.broadinstitute.org/test/genomes/NC_003112.genome</a></td>
<td align="center">NC_003112</td>
</tr>
<tr>
<td align="center">N. Meningitidis (Z2491)</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.broadinstitute.org/test/genomes/NC_003116.genome">https://s3.amazonaws.com/igv.broadinstitute.org/test/genomes/NC_003116.genome</a></td>
<td align="center">NC_003116</td>
</tr>
<tr>
<td align="center">P. falciparum 3D7 (V9.0)</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/Pf3D7_v9.0.genome">https://s3.amazonaws.com/igv.broadinstitute.org/genomes/Pf3D7_v9.0.genome</a></td>
<td align="center">Pf3D7_v9.0</td>
</tr>
<tr>
<td align="center">Plasmodium (3D7 V24)</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/PlasmoDB_24.genome">https://s3.amazonaws.com/igv.broadinstitute.org/genomes/PlasmoDB_24.genome</a></td>
<td align="center">Plasmodium_24</td>
</tr>
<tr>
<td align="center">Rabbit (oryCun2.0)</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/oryCun2.0.genome">https://s3.amazonaws.com/igv.broadinstitute.org/genomes/oryCun2.0.genome</a></td>
<td align="center">oryCun2.0</td>
</tr>
<tr>
<td align="center">Rat (rn5)</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/rn5.genome">https://s3.amazonaws.com/igv.broadinstitute.org/genomes/rn5.genome</a></td>
<td align="center">rn5</td>
</tr>
<tr>
<td align="center">Rhesus (rheMac3)</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/rheMac3.genome">https://s3.amazonaws.com/igv.broadinstitute.org/genomes/rheMac3.genome</a></td>
<td align="center">rheMac3</td>
</tr>
<tr>
<td align="center">Rhesus (rheMac8)</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/rheMac8.genome">https://s3.amazonaws.com/igv.broadinstitute.org/genomes/rheMac8.genome</a></td>
<td align="center">rheMac8</td>
</tr>
<tr>
<td align="center">Rhesus (Mmul_10/rheMac10)</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.org.genomes/rheMac10/rheMac10.genome">https://s3.amazonaws.com/igv.org.genomes/rheMac10/rheMac10.genome</a></td>
<td align="center">rheMac10</td>
</tr>
<tr>
<td align="center">S. cerevisiae (Y55)</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/Y55.genome">https://s3.amazonaws.com/igv.broadinstitute.org/genomes/Y55.genome</a></td>
<td align="center">Y55</td>
</tr>
<tr>
<td align="center">S. pombe (ASM294v2)</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/ASM294v2.genome">https://s3.amazonaws.com/igv.broadinstitute.org/genomes/ASM294v2.genome</a></td>
<td align="center">ASM294v2</td>
</tr>
<tr>
<td align="center">S. sclerotiorum (sclerotiorum)</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/sclerotiorum.genome">https://s3.amazonaws.com/igv.broadinstitute.org/genomes/sclerotiorum.genome</a></td>
<td align="center">sclerotiorum</td>
</tr>
<tr>
<td align="center">Salmonella enterica str. 14028S</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/NC_016856.genome">https://s3.amazonaws.com/igv.broadinstitute.org/genomes/NC_016856.genome</a></td>
<td align="center">NC_016856</td>
</tr>
<tr>
<td align="center">Salmo salar (ICSASG_v2)</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/GCF_000233375.1.genome">https://s3.amazonaws.com/igv.broadinstitute.org/genomes/GCF_000233375.1.genome</a></td>
<td align="center">GCF_000233375.1</td>
</tr>
<tr>
<td align="center">Sheep (Ovis Aries v3.1)</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/oviAri3.genome">https://s3.amazonaws.com/igv.broadinstitute.org/genomes/oviAri3.genome</a></td>
<td align="center">oviAri3</td>
</tr>
<tr>
<td align="center">Sus Scrofa (Sscrofa10.2/susScr3)</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/susScr3.genome">https://s3.amazonaws.com/igv.broadinstitute.org/genomes/susScr3.genome</a></td>
<td align="center">susScr3</td>
</tr>
<tr>
<td align="center">T. brucei (427 v4.2)</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/tb427_4.2.genome">https://s3.amazonaws.com/igv.broadinstitute.org/genomes/tb427_4.2.genome</a></td>
<td align="center">tb427_4.2</td>
</tr>
<tr>
<td align="center">T. brucei (927 v5.0)</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/tbrucei927_5.0.genome">https://s3.amazonaws.com/igv.broadinstitute.org/genomes/tbrucei927_5.0.genome</a></td>
<td align="center">tbrucei927_5.0</td>
</tr>
<tr>
<td align="center">T. brucei gambiense</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/tbgambi.genome">https://s3.amazonaws.com/igv.broadinstitute.org/genomes/tbgambi.genome</a></td>
<td align="center">tbgambi</td>
</tr>
<tr>
<td align="center">Tomato (2.31)</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/SL2.31.genome">https://s3.amazonaws.com/igv.broadinstitute.org/genomes/SL2.31.genome</a></td>
<td align="center">SL2.31</td>
</tr>
<tr>
<td align="center">Tomato (2.40)</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/SL2.40.genome">https://s3.amazonaws.com/igv.broadinstitute.org/genomes/SL2.40.genome</a></td>
<td align="center">SL2.40</td>
</tr>
<tr>
<td align="center">Trout (CCAF000000000)</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/CCAF000000000.genome">https://s3.amazonaws.com/igv.broadinstitute.org/genomes/CCAF000000000.genome</a></td>
<td align="center">CCAF000000000</td>
</tr>
<tr>
<td align="center">V. vitifera</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/vvinifera.genome">https://s3.amazonaws.com/igv.broadinstitute.org/genomes/vvinifera.genome</a></td>
<td align="center">vvitifera</td>
</tr>
<tr>
<td align="center">X. tropicalis v9.0</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/xenTro9.genome">https://s3.amazonaws.com/igv.broadinstitute.org/genomes/xenTro9.genome</a></td>
<td align="center">xenTro9</td>
</tr>
<tr>
<td align="center">X. laevis (7.1)</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/laevis_7.1.genome">https://s3.amazonaws.com/igv.broadinstitute.org/genomes/laevis_7.1.genome</a></td>
<td align="center">laevis_7.1</td>
</tr>
<tr>
<td align="center">Zea mays (AGPv3.31)</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/AGPv3.31.genome">https://s3.amazonaws.com/igv.broadinstitute.org/genomes/AGPv3.31.genome</a></td>
<td align="center">AGPv3.31</td>
</tr>
<tr>
<td align="center">C. reinhardtii (CC-503 v5.5)</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.org.genomes/Creinhardtii_CC-503_v5.0/2019-03-21_Creinhardtii_CC-503_v5.5.genome">https://s3.amazonaws.com/igv.org.genomes/Creinhardtii_CC-503_v5.0/2019-03-21_Creinhardtii_CC-503_v5.5.genome</a></td>
<td align="center">2019-03-21_Creinhardtii_CC-503_v5.5</td>
</tr>
<tr>
<td align="center">C. reinhardtii (CC-503 v5.6)</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.org.genomes/C.reinhardtii_CC-503_v5.6+/2019-03-21_Creinhardtii_CC-503_v5.6.genome">https://s3.amazonaws.com/igv.org.genomes/C.reinhardtii_CC-503_v5.6+/2019-03-21_Creinhardtii_CC-503_v5.6.genome</a></td>
<td align="center">2019-03-21_Creinhardtii_CC-503_v5.6</td>
</tr>
<tr>
<td align="center">C. reinhardtii (CC-503 v5.6 Cp+Mt v4.4)</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.org.genomes/Creinhardtii_CC-503_v5.6/2019-03-21_Creinhardtii_CC-503_v5.6_Cp%2BMt_v4.4.genome">https://s3.amazonaws.com/igv.org.genomes/Creinhardtii_CC-503_v5.6/2019-03-21_Creinhardtii_CC-503_v5.6_Cp%2BMt_v4.4.genome</a></td>
<td align="center">2019-03-21_Creinhardtii_CC-503_v5.6_Cp+Mt_v4.4</td>
</tr>
<tr>
<td align="center">Ixodes scapularis JCVI_ISG_i3_1.0 (GCA_000208615.1)</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.org.genomes/tick/GCA_000208615.1/GCA_000208615.1.genome">https://s3.amazonaws.com/igv.org.genomes/tick/GCA_000208615.1/GCA_000208615.1.genome</a></td>
<td align="center">GCA_000208615.1</td>
</tr>
<tr>
<td align="center">Ixodes scapularis ISE6_asm2.2_deduplicated (GCA_002892825.2)</td>
<td align="center"><a href="https://s3.amazonaws.com/igv.org.genomes/tick/GCA_000208615.1/GCA_000208615.1.genome">https://s3.amazonaws.com/igv.org.genomes/tick/GCA_000208615.1/GCA_000208615.1.genome</a></td>
<td align="center">GCA_002892825.2</td>
</tr>
</tbody></table>
<hr>
<h1 id="文章更新记录"><a href="#文章更新记录" class="headerlink" title="文章更新记录"></a>文章更新记录</h1><h2 id="2025-03-26"><a href="#2025-03-26" class="headerlink" title="2025.03.26"></a>2025.03.26</h2><ol>
<li><code>参数说明</code>中id和name的说明有误,已更正。</li>
<li>更新<code>JSON示例</code>为官方示例。</li>
<li>新增<code>IGV的BLAT</code>相关信息。</li>
</ol>
]]></content>
<categories>
<category>Log</category>