Cassis: Detection and refinment of genomic rearrangement breakpoints

Revival of Cassis, previous web page : http://pbil.univ-lyon1.fr/software/Cassis/

User manual

Installation

Requirements :

• Perl
• R
• Ghostscript
• lastz

Note: lastz binary must be put in directory ./lastz/

Usage

perl cassis.pl [options] <table.txt> <type> <dirGR> <dirGO> <outputdir>

or (new since version 2.0)

perl cassis.pl [options] <table.txt> <type> <GR.fasta> <GO.fasta> <outputdir>

Mandatory parameters

• table : tab separated file with orthologous genes or synteny blocks coordinates in both genomes (see expected format in cassis_manual.pdf p.9)
• type : type of table, either G for genes or B for blocks.
• dirGR and dirGO : 1 directory per genome, each contains several fasta files (one for each chromosome or scaffold)
• GR.fasta and GO.fasta [new in version 2.0] : alternatively to dirs and numerous fasta files, the sequences of both genomes can be given as multi-fasta files
• outputdir : output directory (see the different output files in cassis_manual.pdf p.11-15)

Detailed user manual of version 1.0, with description of all other optional parameters in cassis_manual.pdf

Novel features in version 2.0

• lastz level 1
• instead of giving the genome sequences as numerous unique-entry fasta files for each chromosome, we can now give one single multi-fasta file for each genome.

Citation

• Cassis: Detection of genomic rearrangement breakpoints. C. Baudet, C. Lemaitre, Z. Dias, C. Gautier, E. Tannier, M.-F. Sagot. Bioinformatics, 2010 26(15):1897-1898.

• Precise detection of rearrangement breakpoints in mammalian chromosomes. Lemaitre, C., Tannier, E., Gautier, C., and Sagot, M.-F. BMC Bioinformatics, 2008, 9(286), 15 pages.