archive:bioinformatic_tools:abyss
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archive:bioinformatic_tools:abyss [2010/04/11 16:07] karplus tightened wordy sentence |
archive:bioinformatic_tools:abyss [2010/04/15 19:34] galt |
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| 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]].)] | 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 ==== | ||
| + | |||
| + | 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 | ||
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| + | |||
| + | Still need to check out Google sparsehash, | ||
| + | and where openmpi libs are installed. | ||
| + | Have not run configure and make. | ||
| + | Possilby the make install will require sudo, | ||
| + | judging by the example. | ||
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| <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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