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chhylp123 / hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
MIT License
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crushed k-mer graph #590

Closed yurunxian closed 10 months ago

yurunxian commented 10 months ago

Hi,

I'm working on a ~1.6Gb plant genome with ~ 62Gb HiFi reads (generated by PacBio Revio system) and ~100Gb ONT long reads. Although the assembled genome size is close to our pre-estimation and the N50 is satisfying (> 2Mb), the kmer graph in hifiasm log file is quite weird. The log file is attached.

Any suggestions would be greatly appreciated!

Best, Runxian

hifiasm.txt

yurunxian commented 10 months ago

Ah...I found out what happened. The data in my fastq file was somehow self-doubled. For each read, there are always two 100% identity copies, and so does each k-mer. That's why the number of odd-counting kmer is so few.

chhylp123 commented 10 months ago

Sorry for the late reply. Thanks for the input and good to know it works finally.