A version of crAss (cross assembly) modified to support RPKM (Reads Per Kilobase per Million mapped reads).
This is particularly useful in viral metagenomics, and can be used to generate normalized heatmaps of contigs.
This is derived from the original GPLv3 licensed code from: Reference-independent comparative metagenomics using cross-assembly: crAss Bas E. Dutilh et al. 2012
Run crAss as follows: perl crAss.pl input_directory
The input directory should contain the metagenomic reads (one file per metagenome) and a cross-assembly ACE file. Reads files can be in FASTA format (extensions: .fasta .fna or .fa) or FASTQ format (extensions: .fastq or .fq). Note that read identifiers should be unique across all the files.
For further info please visit the crAss website at http://edwards.sdsu.edu/crass/
The PERL script calls the following programs:
- BioNJ http://www.atgc-montpellier.fr/bionj/
- GNUPlot http://www.gnuplot.info/
- GhostScript http://www.ghostscript.com/
- DrawTree http://evolution.genetics.washington.edu/phylip/doc/drawtree.html Make sure these programs are available and executable from your command line, in the same directory as crAss.pl.
Copyright (C) 2012 Nick Semenkovich (@semenko) semenko@alum.mit.edu, Gordon Lab, Washington University School of Medicine in St. Louis Copyright (C) 2012 Bas E. Dutilh
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.