Banana Slug Genomics

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====== 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 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 ====

Get the appropriate source files to be compiled:

<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>

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>

==== 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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