improve_assembly - Given an assembly, some reads and optionally a reference, reduce the number of contigs and fill gaps.
version 1.160490
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
Andrew J. Page <ap13@sanger.ac.uk>
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
To install Bio::AssemblyImprovement, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::AssemblyImprovement
CPAN shell
perl -MCPAN -e shell install Bio::AssemblyImprovement
For more information on module installation, please visit the detailed CPAN module installation guide.