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De novo transcriptome assembler for short reads
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dzerbino/oases
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README.TXT OASES SOURCE Feb 1, 2010 Daniel Zerbino (dzerbino@soe.ucsc.edu) Marcel Schulz (marcel.schulz@molgen.mpg.de) > SUMMARY * A/ REQUIREMENTS * B/ COMPILING INSTRUCTIONS * C/ RUNNING ---------------------------------------------------------------------------------- A/ REQUIREMENTS Oases should function on any standard 64bit Linux environment with gcc. A good amount of physical memory (12GB to start with, more is no luxury) is recommended. Before trying to compile Oases, you must install the Velvet package: www.ebi.ac.uk/~zerbino/velvet/ . Keep note of the directory in which you install Velvet. ---------------------------------------------------------------------------------- B/ COMPILING INSTRUCTIONS Normally, with a GNU environment, just type: > make 'VELVET_DIR=/path/to/velvet' Note that you need to communicate all the Velvet compilation settings during the Oases compilation. Therefore, if you want to make a debugging colorspace version of Oases with a maximum kmer length of 63 and 5 short-read libraries, the commandline becomes: > make colordebug 'VELVET_DIR=/path/to/velvet' 'MAXKMERLENGTH=63'\ 'CATEGORIES=5' ---------------------------------------------------------------------------------- C/ RUNNING The compilation should have produced a file names OasesManual.pdf with all you could want to know about running Oases.
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