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.