De novo transcriptome assembly with ABySS Export

@article{citeulike:4867928, abstract = {Motivation: Whole transcriptome shotgun sequencing data from non-normalized samples offer unique opportunities to study the metabolic states of organisms. One can deduce gene expression levels using sequence coverage as a surrogate, identify coding changes or discover novel isoforms or transcripts. Especially for discovery of novel events, de novo assembly of transcriptomes is desirable. Results: Transcriptome from tumor tissue of a patient with follicular lymphoma was sequenced with 36 base pair (bp) single- and paired-end reads on the Illumina Genome Analyzer II platform. We assembled [\~{}]194 million reads using ABySS into 66 921 contigs 100 bp or longer, with a maximum contig length of 10 951 bp, representing over 30 million base pairs of unique transcriptome sequence, or roughly 1\% of the genome. Availability and Implementation: Source code and binaries of ABySS are freely available for download at http://www.bcgsc.ca/platform/bioinfo/software/abyss. Assembler tool is implemented in C++. The parallel version uses Open MPI. ABySS-Explorer tool is implemented in Java using the Java universal network/graph framework. Contact: ibirol@bcgsc.ca 10.1093/bioinformatics/btp367}, author = {Birol, Inanc and Jackman, Shaun D. and Nielsen, Cydney B. and Qian, Jenny Q. and Varhol, Richard and Stazyk, Greg and Morin, Ryan D. and Zhao, Yongjun and Hirst, Martin and Schein, Jacqueline E. and Horsman, Doug E. and Connors, Joseph M. and Gascoyne, Randy D. and Marra, Marco A. and Jones, Steven J. M.}, booktitle = {Bioinformatics}, citeulike-article-id = {4867928}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/bioinformatics/btp367}, citeulike-linkout-1 = {http://bioinformatics.oxfordjournals.org/content/25/21/2872.abstract}, citeulike-linkout-2 = {http://bioinformatics.oxfordjournals.org/content/25/21/2872.full.pdf}, citeulike-linkout-3 = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/21/2872}, citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/19528083}, citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=19528083}, day = {1}, doi = {10.1093/bioinformatics/btp367}, journal = {Bioinformatics}, keywords = {assembly, de, novo, rna-seq, transcriptome}, month = {November}, number = {21}, pages = {2872--2877}, posted-at = {2009-11-06 17:21:55}, priority = {2}, title = {De novo transcriptome assembly with ABySS}, url = {http://dx.doi.org/10.1093/bioinformatics/btp367}, volume = {25}, year = {2009} }

TY - JOUR ID - citeulike:4867928 L3 - citeulike-article-id:4867928 N2 - Motivation: Whole transcriptome shotgun sequencing data from non-normalized samples offer unique opportunities to study the metabolic states of organisms. One can deduce gene expression levels using sequence coverage as a surrogate, identify coding changes or discover novel isoforms or transcripts. Especially for discovery of novel events, de novo assembly of transcriptomes is desirable. Results: Transcriptome from tumor tissue of a patient with follicular lymphoma was sequenced with 36 base pair (bp) single- and paired-end reads on the Illumina Genome Analyzer II platform. We assembled [~]194 million reads using ABySS into 66 921 contigs 100 bp or longer, with a maximum contig length of 10 951 bp, representing over 30 million base pairs of unique transcriptome sequence, or roughly 1% of the genome. Availability and Implementation: Source code and binaries of ABySS are freely available for download at http://www.bcgsc.ca/platform/bioinfo/software/abyss. Assembler tool is implemented in C++. The parallel version uses Open MPI. ABySS-Explorer tool is implemented in Java using the Java universal network/graph framework. Contact: ibirol@bcgsc.ca 10.1093/bioinformatics/btp367 IS - 21 JF - Bioinformatics EP - 2877 TI - De novo transcriptome assembly with ABySS VL - 25 T2 - Bioinformatics SP - 2872 KW - assembly KW - de KW - novo KW - rna-seq KW - transcriptome AU - Birol, Inanc AU - Jackman, Shaun AU - Nielsen, Cydney AU - Qian, Jenny AU - Varhol, Richard AU - Stazyk, Greg AU - Morin, Ryan AU - Zhao, Yongjun AU - Hirst, Martin AU - Schein, Jacqueline AU - Horsman, Doug AU - Connors, Joseph AU - Gascoyne, Randy AU - Marra, Marco AU - Jones, Steven PY - 2009/11/01/ UR - http://dx.doi.org/10.1093/bioinformatics/btp367 ER -