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scaffold_with_sspace -a contigs.fa -f 123_1.fastq -r 123_2.fastq -t 2

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

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

# This help message
scaffold_with_sspace -h

USAGE

$debug           ||= 0;
$insert_size     ||= 250;
$threads		 ||= 1;
$scaffolder_exec ||= '/software/pathogen/external/apps/usr/local/SSPACE-BASIC-2.0_linux-x86_64/SSPACE_Basic_v2.0.pl';
$scaffolder_exec = 'SSPACE_Basic_v2.0.pl' unless(Bio::AssemblyImprovement::Validate::Executable->new()->does_executable_exist($scaffolder_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::Scaffold::SSpace::Iterative->new(
    input_files     => $preprocess_input_files->processed_input_files,
    input_assembly  => $preprocess_input_files->processed_input_assembly,
    insert_size     => $insert_size,
    threads			=> $threads,
    scaffolder_exec => $scaffolder_exec,
    debug           => $debug,
    output_base_directory => $output_directory
)->run();

# sort contigs by length
my $scaffolding_output = $iterative_scaffolding->final_output_filename;
my $order_contigs = Bio::AssemblyImprovement::Util::OrderContigsByLength->new( input_filename  => $scaffolding_output );
$order_contigs->run();

__END__

=pod

=encoding UTF-8

=head1 NAME

scaffold_with_sspace - Given an assembly and some reads in fastq format, try and scaffold the assembly.

=head1 VERSION

version 1.160490

=head1 SYNOPSIS

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

   # outputs a file called contigs.scaffolded.fa
   scaffold_with_sspace -a contigs.fa -f 123_1.fastq -r 123_2.fastq 

   # use two threads (default 1)
   scaffold_with_sspace -a contigs.fa -f 123_1.fastq -r 123_2.fastq -t 2
   
   # Gzipped input files are accepted
   scaffold_with_sspace -a contigs.fa.gz -f 123_1.fastq.gz -r 123_2.fastq.gz

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

   # This help message
   scaffold_with_sspace -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