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chhylp123 / hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
MIT License
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Hifiasm Assembly Purging #667

Open Kasturi0312 opened 4 months ago

Kasturi0312 commented 4 months 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 4 months ago

Some short redundant fragments will be removed after purging

chhylp123 commented 4 months ago

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