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shenwei356 / unikmer

A versatile toolkit for k-mers with taxonomic information
https://bioinf.shenwei.me/unikmer
MIT License
75 stars 7 forks source link

Request for more instructions in README.md on hashes #23

Closed jelber2 closed 3 years ago

jelber2 commented 3 years ago

Hi,

Very cool tool, and in go-lang! I would suggest adding some instructions on how to use hash-based "mer" operations. For example when specifying minimizers, syncmers, or k>32 (I think), one needs to provide the reference (or original FASTA/FASTQ sequence) after the unikmer count step for unikmer view to view original sequence with the -g original.fasta.gz flag. With at least cf2a224, this is only clear when playing around with the unikmer view --help and/or trial and error.

shenwei356 commented 3 years ago

Sorry for the late reply, I missed this issue.

The minimizer/syncmers part mainly acts as a library for another project, which I'll make public soon.

In the unikmer tool, the usefulness of minimizer/syncmers are limited right now, but I'll continue to explore them soon after I finished the other project. And more documents will be available.

shenwei356 commented 3 years ago

For example when specifying minimizers, syncmers, or k>32 (I think), one needs to provide the reference (or original FASTA/FASTQ sequence) after the unikmer count step for unikmer view to view original sequence with the -g original.fasta.gz flag.

I've also added a little example.

shenwei356 commented 3 years ago

also released a new version. https://github.com/shenwei356/unikmer/releases/tag/v0.18.7

jelber2 commented 3 years ago

Cool! Thank you!