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.
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.
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:![image](https://github.com/chhylp123/hifiasm/assets/34698068/5768cc1e-9fb7-46c0-be9d-88968a66fe60)
TGS survey:![image](https://github.com/chhylp123/hifiasm/assets/34698068/f90f42c8-bcea-423d-b2fd-c61ec81c1c05)
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.