NAME

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

VERSION

version 1.132610

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

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