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chhylp123 / hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
MIT License
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The genome size of p_ctg.fa is smaller than survey #669

Open Pengzw0909 opened 5 months ago

Pengzw0909 commented 5 months ago

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

TGS survey: image

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.

chhylp123 commented 4 months ago

2.2 Gb assembly with purged might be right?

Pengzw0909 commented 4 months ago

2.2 Gb assembly with purged might be right?

The final genome is 1.8G，it‘s too small.