NAME

Bio::AssemblyImprovement::FillGaps::GapFiller::Main - Run a single iteration of gapfiller

VERSION

version 1.133090

SYNOPSIS

Run a single iteration of gapfiller.

   use Bio::AssemblyImprovement::FillGaps::GapFiller::Main;

   my $config_file_obj = Bio::AssemblyImprovement::Scaffold::SSpace::Main->new(
     input_files => ['abc_1.fastq', 'abc_2.fastq'],
     input_assembly => 'contigs.fa'
     insert_size => 250,
     merge_size => 5,
     threads => 2,
     gap_filler_exec => '/path/to/SSPACE.pl',

     _output_prefix => 'gapfilled'
   )->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