option to include non-canonical k-mers

refresh-bio / kmer-db

Kmer-db is a fast and memory-efficient tool for large-scale k-mer analyses (indexing, querying, estimating evolutionary relationships, etc.).

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option to include non-canonical k-mers #25

Open haneubau opened 7 months ago

haneubau commented 7 months ago

Hi, I was wondering if it is possible to include an argument in kmer-db that allows the inclusion of non-canonical k-mers in the construction and querying of databases. Thus far I have been using a modified version that only uses non-canonical k-mers by simply changing this line: https://github.com/refresh-bio/kmer-db/blob/04f2dd420ea1bb3de263e4753f4cbc154e32b925/src/kmer_extract.h#L87 to kmer_can = kmer_str; Also, thanks for creating kmer-db, it's been quite useful!

best, Hannes

agudys commented 5 months ago

Dear Hannes!

Sorry for the delay. We are planning to publish new Kmer-db release in the next few weeks. We will include an option for inclusion of non canonical k-mers.

Best, Adam