ABI's SOLiD de novo pipeline

This package is now installed at:

/home/scott/Downloads/solidDenovo/denovo2. Caution - Scott installed this with velvet 0.7.62, not 0.7.55 (which is the version the ABI tools were built assuming). It seems to work fine, with minor differences based on re-analyzing ABI's install test data (one less contig, bigger N50).

Documentation on the pipeline can be found in this pdf file: http://gsaf.cssb.utexas.edu/wiki/images/7/71/DeNovo_Assembly_Pipeline_2.0.pdf

Documentation on doing de novo assembly with SOLiD can be found in this pdf file: http://gsaf.cssb.utexas.edu/wiki/images/5/5f/DeNovoAssemblyProtocol0060810.pdf

NOTE: The examples shown for mate-pair (or paired-end) assembly with quality values are INCORRECT - you must put "-r3qv" in front of the r3 quality value information (or -f5qv for PE data).