Selecting sequences from a multi-fasta with certain kmers

Question

[michberr8]

Hi,

I have a fasta file with about 30 9-mers. I also have some metagenomes in fasta format which are about 15 GB (~100 million reads, 125 bp) I would like to use my kmer file to filter out sequences from my metagenomes that only have a match to one of the kmers.

There's a lot of kmer counting software out there like jellyfish, tallymer, meryl, but as far as I can tell, none of these have the utility to select or filter sequences based on the presence of kmers.

Does anyone know of software that would do this efficiently?

Thanks

[GenoMax]

BBduk from BBMap should be able to do this.

[Pierre Lindenbaum]

that only have a match to one of the kmers.

do you mean

ONE hit match => discard SAME kmer found twice => keep TWO different kmer => keep

?

[michberr8]

Sorry, i meant one or more matches to my set of 30 kmers