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

sub 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});

sub 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

sub 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.