NAME Bio::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. METHODS Bio::Kmer->new($filename, \%options) 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}); $kmer->query($queryString) Query the set of kmers with your own query Arguments: query (string) Returns: Count of kmers. 0 indicates that the kmer was not found. -1 indicates an invalid kmer (e.g., invalid length) $kmer->histogram() Count the frequency of kmers. Arguments: none Returns: Reference to an array of counts. The index of the array is the frequency. $kmer->union($kmer2) Finds the union between two sets of kmers Arguments: Another Bio::Kmer object Returns: List of kmers $kmer->intersection($kmer2) Finds the intersection between two sets of kmers Arguments: Another Bio::Kmer object Returns: List of kmers $kmer->subtract($kmer2) Finds the set of kmers unique to this Bio::Kmer object. Arguments: Another Bio::Kmer object Returns: List of kmers COPYRIGHT AND LICENSE MIT license. Go nuts. AUTHOR Author: Lee Katz For additional help, go to https://github.com/lskatz/Bio--Kmer