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chhylp123 / hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
MIT License
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Is x20 of Hifi data enough to construct draft assembly of 6.5Gb genome? #640

Open Jung19911124 opened 4 months ago

Jung19911124 commented 4 months ago

I am involved in a genome project for a wild animal species with a huge genome (6.5 Gb). We expect the genome to be highly heterozygous, and perhaps over half of it will be repetitive sequences.

Due to budget constraints, we could only obtain x80 coverage of CLR, x20 of Hifi data, and x150 of short-read data. We plan to mainly use HiFi data using the CLR-derived assembly as a reference.

I saw this wiki and knew that Hifiam requires at least x13 coverage for each haplotype.

Since the genome sequence of this species have not been determined, we do not need to phase haplotypes and can accord collapsing the haplotypes.

In our case, is x20 of Hifi data enough to construct draft assembly?

chhylp123 commented 4 months ago

You can have a try. As long as hifiasm could find correct peaks, it shoul work. You can also do quick test using tools like https://github.com/schatzlab/genomescope.