CPAN

NAME

Kmer

SYNOPSIS

A module for helping with kmer analysis.

  use strict;
  use warnings;
  use Kmer;
  
  my $kmer=Kmer->new("file.fastq.gz",{kmerCounter=>"jellyfish",numcpus=>4});
  my $kmerHash=$kmer->count();
  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=Kmer->new("file.fastq.gz",{kmerCounter=>"jellyfish",numcpus=>4});

count

Count kmers. If Jellyfish is found, then it will be used. Otherwise, pure perl will be used which is slower.

  Arguments: none
  Returns:   Reference to a hash of kmers where the key is
             the kmer, and the value is count

histogram

Count kmers. If Jellyfish is found, then it will be used. Otherwise, pure perl will be used which is slower.

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