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fill_gaps_with_gapfiller -a contigs.fa -f 123_1.fastq -r 123_2.fastq 

# use two threads (default 1)
fill_gaps_with_gapfiller -a contigs.fa -f 123_1.fastq -r 123_2.fastq -t 2

# Gzipped input files are accepted
fill_gaps_with_gapfiller -a contigs.fa.gz -f 123_1.fastq.gz -r 123_2.fastq.gz

# Insert size defaults to 250 if not specified
fill_gaps_with_gapfiller -a contigs.fa -f 123_1.fastq -r 123_2.fastq -i 3000

# This help message
fill_gaps_with_gapfiller -h

USAGE

$debug           ||= 0;
$insert_size     ||= 250;
$threads		 ||= 1;
$gapfiller_exec ||= '/software/pathogen/external/apps/usr/local/GapFiller_v1-11_linux-x86_64/GapFiller.pl';
$gapfiller_exec = 'GapFiller.pl' unless(Bio::AssemblyImprovement::Validate::Executable->new()->does_executable_exist($gapfiller_exec));

$output_directory ||= getcwd();
make_path($output_directory);

my @input_files = ( $forward_reads_file, $reverse_reads_file );

my $preprocess_input_files = Bio::AssemblyImprovement::Scaffold::SSpace::PreprocessInputFiles->new(
    input_files    => \@input_files,
    input_assembly => $assembly_file
);
my $process_input_files_tmp_dir_obj = $preprocess_input_files->_temp_directory_obj();

my $iterative_scaffolding = Bio::AssemblyImprovement::FillGaps::GapFiller::Iterative->new(
    input_files     => $preprocess_input_files->processed_input_files,
    input_assembly  => $preprocess_input_files->processed_input_assembly,
    insert_size     => $insert_size,
    threads			=> $threads,
    gap_filler_exec  => $gapfiller_exec,
    debug           => $debug,
    _output_prefix  => 'gapfilled',
    output_base_directory => $output_directory
)->run();

__END__

=pod

=encoding UTF-8

=head1 NAME

fill_gaps_with_gapfiller - Given an assembly iteratively fill gaps

=head1 VERSION

version 1.160490

=head1 SYNOPSIS

Given an assembly and some reads in fastq format, try and fill in the gaps. Do multiple iterations with different values, and cleanup all intermediate files.

   # outputs a file called contigs.scaffolded.fa
   fill_gaps_with_gapfiller -a contigs.fa -f 123_1.fastq -r 123_2.fastq 
   
   # use two threads (default 1)
   fill_gaps_with_gapfiller -a contigs.fa -f 123_1.fastq -r 123_2.fastq -t 2

   # Gzipped input files are accepted
   fill_gaps_with_gapfiller -a contigs.fa.gz -f 123_1.fastq.gz -r 123_2.fastq.gz

   # Insert size defaults to 250 if not specified
   fill_gaps_with_gapfiller -a contigs.fa -f 123_1.fastq -r 123_2.fastq -i 3000

   # This help message
   fill_gaps_with_gapfiller -h

=head1 AUTHOR

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

=head1 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

=cut