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--- archive:bioinformatic_tools:abyss [2010/04/07 20:04]
galt
+++ archive:bioinformatic_tools:abyss [2010/04/09 22:47]
cbrumbau Merged publications into Overview
@@ Line 1: / Line 1: @@
-===== ABySS =====
+====== ABySS ======
-====High Level Overview====
-ABySS - Assembly By Short-read Sequence.
-Parallel version uses MPI and can assemble larger genomes.
-  Genome Res. 2009 Jun;19(6):1117-23. Epub 2009 Feb 27.
+===== Overview =====
-  ABySS: a parallel assembler for short read sequence data.
+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]].
-  Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I.
+)] stands for **A**ssembly **By** **S**hort **S**equences.
-  Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 4E6, Canada.
-[[http://genome.cshlp.org/content/19/6/1117.long|Free full text]]
-ABySS binaries and documentation are available [[http://www.bcgsc.ca/platform/bioinfo/software/abyss|here]].
+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 deployed in a following paper when 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 ====
+[[http://www.bcgsc.ca/platform/bioinfo/software/abyss]]
+==== Source with Binaries and Documentation ====
+[[http://www.bcgsc.ca/platform/bioinfo/software/abyss/releases]]
+===== References =====
+<refnotes>notes-separator: none</refnotes>
+~~REFNOTES cite~~

Banana Slug Genomics

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