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.gitignore
.gitignore
 
 
1.01_StringBasics.ipynb
1.01_StringBasics.ipynb
 
 
1.02_ManipulatingDNAStrings.ipynb
1.02_ManipulatingDNAStrings.ipynb
 
 
1.03_ParsingRefGenome.ipynb
1.03_ParsingRefGenome.ipynb
 
 
1.04_WorkingWithSequencingReads.ipynb
1.04_WorkingWithSequencingReads.ipynb
 
 
1.05_AnalyzingReadsByPosition.ipynb
1.05_AnalyzingReadsByPosition.ipynb
 
 
1.06_NaiveExactMatching-MatchingArtificialReads.ipynb
1.06_NaiveExactMatching-MatchingArtificialReads.ipynb
 
 
1.07_NaiveExactMatching-MatchingRealReads.ipynb
1.07_NaiveExactMatching-MatchingRealReads.ipynb
 
 
2.01_BoyerMoore.ipynb
2.01_BoyerMoore.ipynb
 
 
2.02_SubstringIndex.ipynb
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2.03_ApproximateMatching.ipynb
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3.01_EditDistanceDP.ipynb
3.01_EditDistanceDP.ipynb
 
 
3.02_GlobalAlignment.ipynb
3.02_GlobalAlignment.ipynb
 
 
3.03_FindingOverlaps.ipynb
3.03_FindingOverlaps.ipynb
 
 
3.04_FindingAllOverlaps.ipynb
3.04_FindingAllOverlaps.ipynb
 
 
4.01_ShortestCommonSuperstring.ipynb
4.01_ShortestCommonSuperstring.ipynb
 
 
4.02_GreedySCS.ipynb
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4.03_DeBruijn.ipynb
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ERR266411_1.for_asm.fastq
ERR266411_1.for_asm.fastq
 
 
README.md
README.md
 
 
SRR835775_1.first1000.fastq
SRR835775_1.first1000.fastq
 
 
ads1_week4_reads.fq
ads1_week4_reads.fq
 
 
bm_preproc.py
bm_preproc.py
 
 
bm_preproc.pyc
bm_preproc.pyc
 
 
chr1.GRCh38.excerpt.fasta
chr1.GRCh38.excerpt.fasta
 
 
homework-1.ipynb
homework-1.ipynb
 
 
homework-2.ipynb
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homework-3.ipynb
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homework-4.ipynb
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hw1.py
hw1.py
 
 
lambda_virus.fa
lambda_virus.fa
 
 
phix.fa
phix.fa
 
 

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Algorithms-for-DNA-sequencing

Copies of notebooks used in the practical sessions for Algorithms for DNA Sequencing

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Codes from Coursera's course Algorithms for DNA sequencing, part of genomic data science specialization offered by Johns Hopkins University

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  • Jupyter Notebook 94.8%
  • Python 5.2%