NAME

improve_assembly - Given an assembly, some reads and optionally a reference, reduce the number of contigs and fill gaps.

VERSION

version 1.160490

SYNOPSIS

Given an assembly, some reads and optionally a reference, reduce the number of contigs and fill gaps.

# Improve the assembly without a reference
improve_assembly -a contigs.fa -f 123_1.fastq -r 123_2.fastq

# Provide a reference
improve_assembly -a contigs.fa -f 123_1.fastq -r 123_2.fastq  -c my_reference.fa

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

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

# Output to a specific directory
improve_assembly -a contigs.fa -f 123_1.fastq -r 123_2.fastq -o my_directory

# This help message
improve_assembly -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