Rnnotator is an automated software pipeline that generates transcript models by de novo assembly of RNA-Seq data without the need for a reference genome.
Rnnotator must be run on a 64-bit Linux architecture. Before running Rnnotator the following prerequisites must be installed:
- Blat v. 34 (http://genome.ucsc.edu/FAQ/FAQblat.html#blat3) -- DONE
- Velvet 1.0.15 (http://www.ebi.ac.uk/~zerbino/velvet/) -- DONE
- AMOS (http://sourceforge.net/apps/mediawiki/amos/index.php) -- DONE
- Vmatch 2.0 (http://www.vmatch.de/) -- DONE
- bwa 0.5.8c (http://bio-bwa.sourceforge.net/) -- DONE
- MUMmer (http://sourceforge.net/projects/mummer/) -- DONE
- BioPerl (http://www.bioperl.org) -- base system
- Perl modules: Parallel::ForkManager, Tree (http://search.cpan.org/) -- DONE
Optional prerequisites are:
- Oases 0.1.18 (http://www.ebi.ac.uk/~zerbino/oases/) -- DONE
- Bambus 2.33 (http://www.cbcb.umd.edu/software/bambus/)
- Sopra 1.0 (dayarian@physics.rutgers.edu) x1 – x4 scripts
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