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MatthewRalston / kmerdb

Python bioinformatics CLI for k-mer counts and de Bruijn graphs
https://matthewralston.github.io/kmerdb
Apache License 2.0
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vsearch conda package #131

Open MatthewRalston opened 7 months ago

MatthewRalston commented 7 months ago

Might suggest the use of conda package [vsearch](https://github.com/torognes/vsearch/) to merge reads into 'contigs' i.e. inserts.

MatthewRalston commented 3 months ago

Have been reviewing k-mer literature because of the search algorithm. I think I can write my own smith-waterman alignment variant on search alignment and seeding/match optimizer and heuristic which is based on k-mer indices.

The obvious option is on-disk (index+cache based) matching for k-mers but that seems over engineered, so maybe a much simpler k-mer seed region matching strategy is needed for the aligner.