what input should we have, forward reads or reverse reads or both?

will-rowe / hulk

Histosketching Using Little Kmers

MIT License

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what input should we have, forward reads or reverse reads or both? #19

Closed jianshu93 closed 2 years ago

jianshu93 commented 2 years ago

Hello Hulk developers,

I am curious what input we should offer to hulk sketch for pair-end metagenomic sequencing, interleaved reads, or just forward reads? For mash, I use interleaved reads (both forward and reverse reads).

Thanks,

Jianshu

will-rowe commented 2 years ago

Hi Jianshu,

HULK doesn't take into account paired-end information, so you can provide an interleaved file, a FASTQ stream or several files.

Hope that helps,

Will