search

chhylp123 / hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
MIT License
502 stars 84 forks source link

Hifiasm Assembly Purging #667

Open Kasturi0312 opened 2 weeks ago

Kasturi0312 commented 2 weeks ago

I have a homozygous genome. so it is suggested to run the assembly with -l0. When i run the assembly with purging as 0 the N50 value is 15mb. but whwn i run the assembly with purging as 2 , the N50 value becomes 19mb . why is it the case that assembly with aggressive purging gives a better assembly?

Weihankk commented 1 week ago

Some short redundant fragments will be removed after purging

chhylp123 commented 6 days ago

@Kasturi0312 Purging is a little bit risky. It may incorrectly collapse repeats to make N50 larger.