Finding all positions for all kmers belonging to a (not so short) list of kmers in a large genome

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5.7 years ago

jyu429 ▴ 120

Hi,

Is there a tool for not only enumerating the counts of kmers (like jellyfish) but also will list their positions? I know its much more exhausting memory-wise but I'm looking for the best way to do this, even if a tool doesn't exist currently.

Thanks!

genome sequencing kmer • 1.9k views

ADD COMMENT • link updated 5.7 years ago by ATpoint 85k • written 5.7 years ago by jyu429 ▴ 120

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Take a look at Finding 16 mer not present in GRCh38. In this a suggestion was to use bowtie to align the kmers against the genome. I would do the alignment and then filter for matches with 100% sequence identity. It might help to set gap opening and mismatch penalties to like 10000 to only retain perfect matches.

ADD REPLY • link 5.7 years ago by ATpoint 85k

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Is that really faster than for example implementing a search trie?

ADD REPLY • link 5.7 years ago by jyu429 ▴ 120

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How large your Kmers?, all combinations?, all occurrences? I used to code some scripts in Perl for kmer counting (8-12 kmers) with their position for cis-regulatory elements in some plant genomes, so it is not hard to do, even on the 2 GB RAM machine I had.

ADD REPLY • link 5.7 years ago by JC 13k

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