The genome size of p_ctg.fa is smaller than survey
Pengzw0909 opened this issue · comments
Hi,
I did a NGS survey and a TGS survey, the estimated size is about 2.2Gb.The genome size of p_ctg.fa is 1.69Gb
, smaller than survey. Can you give me some suggestion？ It‘s an insect of diptera.
NGS survey:
TGS survey:
cmd:
fa=ccs.fasta
~/01.software/hifiasm/hifiasm-0.19.8/hifiasm -o hifiasm.asm -t60 -l 2 -n 4 $fa 2> $prefix.assemble.log
p_ctg.fa:
Contigs stat:
CtgNum CtgLen CtgN50 CtgN90 CtgMax GC(%)
1029 1693753142 18588588 2976463 107319031 39.83
the log is
assemble.log
So I have changed the parameter “--hom-cov=57”，the genome size is 2.8Gb, but I found that there was a lot of redundancy. After purge，the genome size is smaller than 2.2Gb.
2.2 Gb assembly with purged might be right?
2.2 Gb assembly with purged might be right?
The final genome is 1.8G，it‘s too small.