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Software to identify overrepresented k-mers in sequencing data

Hi all,

I need to identify overrepresented k-mers in sequencing data. Ideally, I would need k-mers of lengths between 7 and 20 (I am searching for some sequencing adaptors remnants).

Anyone knows of a program able to do this?

Thanks! Federico

sequencing k-mer
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by abascalfederico abascalfederico

1 answer

fastqc with option kmer: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/11%20Kmer%20Content.html

   -k --kmers       Specifies the length of Kmer to look for in the Kmer content
                    module. Specified Kmer length must be between 2 and 10. Default
                    length is 7 if not specified.
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written by Pierre Lindenbaum Pierre Lindenbaum

Thanks Pierre! That may be helpful but I would like to be able to search for longer kmers (up to 20 bps)

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written by abascalfederico abascalfederico

fastqc is a shell script, change the following lines:

if ($kmer_size) {
    unless ($kmer_size =~ /^\d+$/) {
        die "Kmer size '$kmer_size' was not a number";
    }
    #### CHANGE 10 to WHATEVER...
    if ($kmer_size < 2 or $kmer_size > 10) {
        die "Kmer size must be in the range 2-10";
    }

    push @java_args,"-Dfastqc.kmer_size=$kmer_size";
}

use at your own risk.

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written by Pierre Lindenbaum Pierre Lindenbaum

Minimum at 2 obviously makes sense. Any idea why they hard-coded the maximum at 10?

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written by igor igor

because 10 is not 'too much' in memory: there is potentialy 4^10= 10,48,576 unique keys in the map. k=20 would be : 1,099,511,627,776 ==> OUT OF MEMORY.

• 1 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

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