Accuracy of assembly had a big problem

[Shokusei]

Hi, @swacisko
I tried to assemble a short-read genome of Eleocharis vivipara.
I was expecting to get accurate assembled genome data, but I couldn't get ideal data this time.
In detail,

1. the BUSCO data was insufficient as below,

C:4.8%[S:4.2%,D:0.6%],F:20.8%,M:74.4%,n:1614
77 Complete BUSCOs (C)
67 Complete and single-copy BUSCOs (S)
10 Complete and duplicated BUSCOs (D)
336 Fragmented BUSCOs (F)
1201 Missing BUSCOs (M)
1614 Total BUSCO (embryophyta_odb10) groups searched

2. The contigs are challenging to use for scaffolding.
   I could get approximately 770,000 contigs through ALGA, but after scaffolding, the number of contigs only reduced to about 450,000.

I want to succeed as I could get good contigs of ice plant before.
I am expecting your help.

[xiekunwhy]

busco is not reliable when assembly is fragmented. Try k-mer base evaluates.