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--- archive:bioinformatic_tools:abyss [2010/04/15 19:34]
galt
+++ archive:bioinformatic_tools:abyss [2010/05/10 22:21]
jstjohn
@@ Line 1: / Line 1: @@
 ====== 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]].)]
+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.
+Note that ABySS is also the recommended assembler by Illumina for large genomes. {{:bioinformatic_tools:abyss_technote_illumina.pdf|Illumina Technote Paper}}
 ==== 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
-  mv abyss-1.1.2 abyss
-  mv abyss-1.1.2.tar.gz abyss/
-  cd abyss
+<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>
-Still need to check out Google sparsehash,
+First, OpenMPI and Google sparsehash need to be compiled and installed for ABySS.
-and where openmpi libs are installed.
-Have not run configure and make.
-Possilby the make install will require sudo,
-judging by the example.
+<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>
-==== Website ====
+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.
-[[http://www.bcgsc.ca/platform/bioinfo/software/abyss]]
-==== Source with Binaries and Documentation ====
+<code>
-[[http://www.bcgsc.ca/platform/bioinfo/software/abyss/releases]]
+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~~

Banana Slug Genomics

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