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chhylp123 / hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

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How to classify hifi reads into haplotype genomes? minimap2 did not work well

DayTimeMouse opened this issue · comments

commented

Hi,

I used HiFi + ONT + HiC reads to assemble haplotype genomes, then I want to classfiy hifi reads into haplotype genome separately.

I have tried to use minimap2, due to the similar haplotype genomes, it did not work well.

I cat hap1 and hap2 into hap1_hap2.fa, use "minimap2(2.27-r1193) -c --secondary=no hap1_hap2.fa hifi.fastq.gz >aln.paf",
then use reads ID from paf file to calculate the precision, only ~0.56. The HiFi reads were simulated, so I know the reads ID real belong to which haplotype.

So, can hifiasm do this? Or, do you have other method for this?

Best wishes.

commented

My understanding is that if your sample has long homozygous regions, minimap2 may not find the best alignment within these regions.

commented

Hi chhylp123,

I noticed that both hap1.gfa and hap2.gfa in the output of hifiasm contain HG:A:m and HG:A:p, why do they contain two kinds of tags? Another problem is that the haplotype tag in gfa only has some reads ids, so how do I get all the haplotype partition reads ids?

Looking forward to your reply.

commented

@DayTimeMouse Please see here: https://hifiasm.readthedocs.io/en/latest/interpreting-output.html#interpreting-output. Currently hifiasm cannot output the information of all reads.