archive:bioinformatic_tools:abyss
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archive:bioinformatic_tools:abyss [2010/04/09 13:34] cbrumbau Added citations |
archive:bioinformatic_tools:abyss [2010/04/15 19:31] galt |
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| )] stands for **A**ssembly **By** **S**hort **S**equences. | )] 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)] | + | 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]].)] |
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| + | ===== Installing ===== | ||
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| + | 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 ==== | ==== Website ==== | ||
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| ==== Source with Binaries and Documentation ==== | ==== Source with Binaries and Documentation ==== | ||
| [[http://www.bcgsc.ca/platform/bioinfo/software/abyss/releases]] | [[http://www.bcgsc.ca/platform/bioinfo/software/abyss/releases]] | ||
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| - | ===== Publications ===== | ||
| - | ABySS deployed in a following paper when used for assembly of the transcriptome from the tumor tissue of a patient with follicular lymphoma: | ||
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| - | 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]]. | ||
| ===== References ===== | ===== References ===== | ||
| <refnotes>notes-separator: none</refnotes> | <refnotes>notes-separator: none</refnotes> | ||
| ~~REFNOTES cite~~ | ~~REFNOTES cite~~ | ||
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archive/bioinformatic_tools/abyss.txt · Last modified: 2015/07/28 06:23 by ceisenhart
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