NAME

Bio::AssemblyImprovement::FillGaps::GapFiller::Iterative - Iteratively close gaps

VERSION

version 1.132610

SYNOPSIS

Iteratively close gaps. Use different mappers in rotation, picking the most confident gaps first

use Bio::AssemblyImprovement::FillGaps::GapFiller::Iterative;

my $iterative_gapfilling = Bio::AssemblyImprovement::Scaffold::SSpace::Iterative->new(
  input_files => ['abc_1.fastq', 'abc_2.fastq'],
  input_assembly => 'contigs.fa'
  insert_size => 250,
  gap_filler_exec => '/path/to/SSPACE.pl',
  merge_sizes => [100,50,30,10],
  threads => 2,
)->run;

METHODS

run

Iteratively run gapfiller.

SEE ALSO

AUTHOR

Andrew J. Page <ap13@sanger.ac.uk>

COPYRIGHT AND LICENSE

This software is Copyright (c) 2012 by Wellcome Trust Sanger Institute.

This is free software, licensed under:

The GNU General Public License, Version 3, June 2007