kmer counting software issue

[Rui Guo]

There are many kmer counting software. If just to find repeats, can I just use someone that can count frequency and can give the kmer position in the genome(or reads), and then align the high frequency kmers? Some software just output the kmer counts, I don't know which software can output the kmer position along with the kmer counts.

[rhinoceros]

You can always map the k-mers back to the genome with e.g. bowtie2..

[Rui Guo]

Thank you. I think mapping back is redundant because when counting it can also do that. I will try to find some other ways to do that.

[rhinoceros]

Thank you. I think mapping back is redundant because when counting it can also do that. I will try to find some other ways to do that.

Saving positional information is a lot of overhead for k-mer counting algorithms so I'm not so sure it has been implemented in any of them..

[colindaven]

For bacterial genomes there is an old program which can do this for 8-14mer kmers called OligoCounter. Not useful for large genomes though (>50 MB?).

http://webhost1.mh-hannover.de/davenport/oligocounter/

Mapping back to the genome is probably a much quicker option.