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====== ABySS ====== ===== Overview ===== ABySS[(cite:abyss>Jared T. Simpson, Kim Wong, Shaun D. Jackman, Jacqueline E. Schein, Steven J.M. Jones, and İnanç Birol. ABySS: A parallel assembler for short read sequence data. //Genome Res.// June 2009 19: 1117-1123; Published in Advance February 27, 2009, doi:[[http://dx.doi.org/10.1101/gr.089532.108|10.1101/gr.089532.108]]. )] stands for **A**ssembly **By** **S**hort **S**equences. ABySS is a //de novo// parallel, paired-end, short read DNA sequence assembler. The single processor version can assemble genomes of up to 100 Mbases.[(cite:website>[[http://www.bcgsc.ca/platform/bioinfo/software/abyss]])] The parallel version uses MPI and can assemble larger genomes.[(cite:website)] It was used for assembly of a transcriptome from the tumor tissue of a patient with follicular lymphoma.[(cite:Biroletal>Inanç Birol, Shaun D. Jackman, Cydney B. Nielsen, Jenny Q. Qian, Richard Varhol, Greg Stazyk, Ryan D. Morin, Yongjun Zhao, Martin Hirst, Jacqueline E. Schein, Doug E. Horsman, Joseph M. Connors, Randy D. Gascoyne, Marco A. Marra, and Steven J. M. Jones. De novo transcriptome assembly with ABySS. //Bioinformatics// 25: 2872-2877. Advance Access published on November 1, 2009, doi:[[http://dx.doi.org/10.1093/bioinformatics/btp367|10.1093/bioinformatics/btp367]].)] ==== Installing ==== cd /campusdata/BME235/programs wget http://www.bcgsc.ca/downloads/abyss/abyss-1.1.2.tar.gz tar xfz abyss-1.1.2.tar.gz mv abyss-1.1.2 abyss mv abyss-1.1.2.tar.gz abyss/ cd abyss ==== Website ==== [[http://www.bcgsc.ca/platform/bioinfo/software/abyss]] ==== Source with Binaries and Documentation ==== [[http://www.bcgsc.ca/platform/bioinfo/software/abyss/releases]] ===== References ===== <refnotes>notes-separator: none</refnotes> ~~REFNOTES cite~~
