NAME

fill_gaps_with_gapfiller - Given an assembly iteratively fill gaps

VERSION

version 1.132610

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

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