archive:bioinformatic_tools:abyss
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archive:bioinformatic_tools:abyss [2010/04/09 13:34] cbrumbau Added citations |
archive:bioinformatic_tools:abyss [2010/05/02 21:17] 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]].)] | ||
| - | ==== Website ==== | + | ABySS can use large kmer values greater than 31. |
| - | [[http://www.bcgsc.ca/platform/bioinfo/software/abyss]] | + | |
| - | ==== Source with Binaries and Documentation ==== | + | ==== Installing ==== |
| - | [[http://www.bcgsc.ca/platform/bioinfo/software/abyss/releases]] | + | |
| - | ===== Publications ===== | + | Get the appropriate source files to be compiled: |
| - | ABySS deployed in a following paper when used for assembly of the transcriptome from the tumor tissue of a patient with follicular lymphoma: | + | |
| - | 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]]. | + | <code> |
| + | cd /campusdata/BME235/programs | ||
| + | wget http://www.bcgsc.ca/downloads/abyss/abyss-1.1.2.tar.gz | ||
| + | wget http://www.open-mpi.org/software/ompi/v1.4/downloads/openmpi-1.4.1.tar.gz | ||
| + | wget http://google-sparsehash.googlecode.com/files/sparsehash-1.7.tar.gz | ||
| + | tar xfz abyss-1.1.2.tar.gz | ||
| + | tar xfz openmpi-1.4.1.tar.gz | ||
| + | tar xfz sparsehash-1.7.tar.gz | ||
| + | mv abyss-1.1.2.tar.gz abyss-1.1.2/ | ||
| + | mv openmpi-1.4.1.tar.gz openmpi-1.4.1/ | ||
| + | mv sparsehash-1.7.tar.gz sparsehash-1.7/ | ||
| + | </code> | ||
| - | ===== References ===== | + | First, OpenMPI and Google sparsehash need to be compiled and installed for ABySS. |
| - | <refnotes>notes-separator: none</refnotes> | + | |
| - | ~~REFNOTES cite~~ | + | |
| + | <code> | ||
| + | cd /campusdata/BME235/programs/openmpi-1.4.1 | ||
| + | ./configure --prefix=/campusdata/BME235 | ||
| + | make | ||
| + | make install | ||
| + | cd /campusdata/BME235/programs/sparsehash-1.7 | ||
| + | ./configure --prefix=/campusdata/BME235 | ||
| + | make | ||
| + | make install | ||
| + | </code> | ||
| + | Next, a [[http://code.google.com/p/google-sparsehash/issues/detail?id=55|patch]] needs to be applied so that ABySS can properly compile with support for Google sparsehash 1.7. This issue will be fixed in the next release of Google sparsehash. | ||
| + | <code> | ||
| + | cd /campusdata/BME235/include/google/sparsehash | ||
| + | wget http://google-sparsehash.googlecode.com/issues/attachment?aid=-5666329961626930947&name=deallocate.diff | ||
| + | patch < deallocate.diff | ||
| + | </code> | ||
| + | Now ABySS can be compiled with OpenMPI and Google sparsehash support. | ||
| + | |||
| + | <code> | ||
| + | cd /campusdata/BME235/programs/abyss-1.1.2 | ||
| + | ./configure --prefix=/campusdata/BME235 CPPFLAGS=-I/campusdata/BME235/include | ||
| + | make | ||
| + | make install | ||
| + | </code> | ||
| + | |||
| + | ==== Websites ==== | ||
| + | [[http://www.bcgsc.ca/platform/bioinfo/software/abyss|ABySS]] \\ | ||
| + | [[http://www.open-mpi.org|OpenMPI]] \\ | ||
| + | [[http://code.google.com/p/google-sparsehash|Google sparsehash]] | ||
| + | |||
| + | ==== Sources with Binaries and Documentation ==== | ||
| + | [[http://www.bcgsc.ca/platform/bioinfo/software/abyss/releases|ABySS]] \\ | ||
| + | [[http://www.open-mpi.org/software/ompi|OpenMPI]] \\ | ||
| + | [[http://code.google.com/p/google-sparsehash/downloads/list|Google sparsehash]] | ||
| + | |||
| + | ===== References ===== | ||
| + | <refnotes>notes-separator: none</refnotes> | ||
| + | ~~REFNOTES cite~~ | ||
archive/bioinformatic_tools/abyss.txt · Last modified: 2015/07/28 06:23 by ceisenhart
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