archive:bioinformatic_tools:abyss
Differences
This shows you the differences between two versions of the page.
| Both sides previous revision Previous revision Next revision | Previous revision Next revision Both sides next revision | ||
|
archive:bioinformatic_tools:abyss [2010/04/15 19:32] galt |
archive:bioinformatic_tools:abyss [2010/05/02 21:17] galt |
||
|---|---|---|---|
| Line 5: | Line 5: | ||
| )] 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)] 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]].)] | ||
| + | |||
| + | ABySS can use large kmer values greater than 31. | ||
| ==== Installing ==== | ==== Installing ==== | ||
| - | cd /campusdata/BME235/programs | + | Get the appropriate source files to be compiled: |
| - | wget http://www.bcgsc.ca/downloads/abyss/abyss-1.1.2.tar.gz | + | |
| - | tar xfz abyss-1.1.2.tar.gz | + | <code> |
| - | mv abyss-1.1.2 abyss | + | cd /campusdata/BME235/programs |
| - | mv abyss-1.1.2.tar.gz abyss/ | + | wget http://www.bcgsc.ca/downloads/abyss/abyss-1.1.2.tar.gz |
| - | cd abyss | + | 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> | ||
| + | |||
| + | First, OpenMPI and Google sparsehash need to be compiled and installed for ABySS. | ||
| + | |||
| + | <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> | ||
| - | ==== Website ==== | + | ==== Websites ==== |
| - | [[http://www.bcgsc.ca/platform/bioinfo/software/abyss]] | + | [[http://www.bcgsc.ca/platform/bioinfo/software/abyss|ABySS]] \\ |
| + | [[http://www.open-mpi.org|OpenMPI]] \\ | ||
| + | [[http://code.google.com/p/google-sparsehash|Google sparsehash]] | ||
| - | ==== Source with Binaries and Documentation ==== | + | ==== Sources with Binaries and Documentation ==== |
| - | [[http://www.bcgsc.ca/platform/bioinfo/software/abyss/releases]] | + | [[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 ===== | ===== References ===== | ||
archive/bioinformatic_tools/abyss.txt · Last modified: 2015/07/28 06:23 by ceisenhart
Except where otherwise noted, content on this wiki is licensed under the following license: CC Attribution-Noncommercial-Share Alike 3.0 Unported
