/ 
Bio_AssemblyImprovement-1.160490
River stage zero No dependents
/ Bio::AssemblyImprovement

NAME

Bio::AssemblyImprovement - Improve an assembly by scaffolding, contig ordering and gap closing.

VERSION

version 1.160490

SYNOPSIS

Take in an assembly in FASTA format,reads in FASTQ format, and optionally a reference and produce a a better reference using Abacas/SSpace and GapFiller.

# 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

SEE ALSO

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