Bio::Kmer(3)

CPAN

NAME
Kmer

SYNOPSIS
A module for helping with kmer analysis.

  use strict;
  use warnings;
  use Bio::Kmer;

  my $kmer=Bio::Kmer->new("file.fastq.gz",{kmercounter=>"jellyfish",numcpus=>4});
  my $kmerHash=$kmer->kmers();
  my $countOfCounts=$kmer->histogram();

DESCRIPTION
A module for helping with kmer analysis. The basic methods help count kmers and can produce a count of counts. Currently this module only supports fastq format. Although this module can count kmers with pure perl, it is recommended to give the option for a different kmer counter such as Jellyfish.

AUTHOR
Author: Lee Katz <lkatz@cdc.gov>

METHODS

new Create a new instance of the kmer counter. One object per file.

      Applicable arguments:
      Argument     Default    Description
      kmercounter  perl       What kmer counter software to use.
                              Choices: Perl, Jellyfish.
      kmerlength   21         Kmer length
      numcpus      1          This module uses perl
                              multithreading with pure perl or
                              can supply this option to other
                              software like jellyfish.
      gt           1          If the count of kmers is fewer
                              than this, ignore the kmer. This
                              might help speed analysis if you
                              do not care about low-count kmers.

      Examples:
      my $kmer=Bio::Kmer->new("file.fastq.gz",{kmercounter=>"jellyfish",numcpus=>4});

histogram
    Count the frequency of kmers.

      Arguments: none
      Returns:   Reference to an array of counts. The index of
                 the array is the frequency.