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chhylp123 / hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
MIT License
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Abnormal Kmer Distribution #189

Open sysy000 opened 2 years ago

sysy000 commented 2 years ago

Dear Authors: Here is my kmer distribution result from the hifiasm v0.15.4 on ccs hifi reads with default paras. There is no peak and I don't know why would this happen. I use the hifi data run assembly, here is my code of ccs to hifi： smrtlink/smrtcmds/bin/ccs -j 30 m64252e_210717_222335.subreads.bam hifi.bam smrtlink/smrtcmds/bin/bam2fasta -o hifi hifi.bam The genome size is about 670Mb, the coverage of hifi reads is around 33×. Could you please give some tips about this ? 1 2 3

chhylp123 commented 2 years ago

Please see: https://hifiasm.readthedocs.io/en/latest/faq.html#why-does-hifiasm-stuck-or-crash .

perla-far commented 2 years ago

Hello, It is better to give Hifiasm as input the Fasta or Fastq fromat. So first convert your data from .bam to .fq using bam2fastq tool and re-run hifiasm using the script in the tutorial. goodluck