NAME

Bio::Minimizer - minimizer package

Based on the ideas put forth by Roberts et al 2004: https://academic.oup.com/bioinformatics/article/20/18/3363/202143

SYNOPSIS

my $minimizer = Bio::Minimizer->new($sequenceString);
my $kmers     = $minimizer->{kmers};     # hash of minimizer => kmer
my $minimizers= $minimizer->{minimizers};# hash of minimizer => [kmer1,kmer2,...]

# hash of minimizer => [start1,start2,...] 
# Start coordinates are on the fwd strand even when
# matched against the rev strand.
my $starts    = $minimizer->{starts}; 

# With more options
my $minimizer2= Bio::Minimizer->new($sequenceString,{k=>31,l=>21});

DESCRIPTION

Creates a set of minimizers from sequence

EXAMPLES

example: Sort a fastq file by minimizer, potentially shrinking gzip size.

This is implemented in this package's scripts/sort*.pl scripts.

use Bio::Minimizer

# Read fastq file via stdin, in this example
while(my $id = <>){
  # Grab an entry
  ($seq,$plus,$qual) = (scalar(<>), scalar(<>), scalar(<>)); 
  chomp($id,$seq,$plus,$qual); 

  # minimizer object
  $MINIMIZER = Bio::Minimizer->new($seq,{k=>length($seq)}); 
  # The only minimizer in this entry because k==length(seq)
  $minMinimizer = (values(%{$$MINIMIZER{minimizers}}))[0]; 

  # combine the minimum minimizer with the entry, for
  # sorting later.
  # Save the entry as a string so that we don't have to
  # parse it later.
  my $entry = [$minMinimizer, "$id\n$seq\n$plus\n$qual\n"];
  push(@entry,$entry);
}

for my $e(sort {$$a[0] cmp $$b[0]} @entry){
  print $$e[1];
} 

METHODS

Bio::Minimizer->new()

Arguments:
  sequence     A string of ACGT
  settings     A hash
    k          Kmer length
    l          Minimizer length (some might call it lmer)
    numcpus    Number of threads to use. (not used)