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 approximately 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.
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 approximately 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.
Authors: Richard H Baker; Apurva Narechania; Philip M Johns; Gerald S Wilkinson Journal: Philos Trans R Soc Lond B Biol Sci Date: 2012-08-19 Impact factor: 6.237
Authors: Malachi Griffith; Obi L Griffith; Jill Mwenifumbo; Rodrigo Goya; A Sorana Morrissy; Ryan D Morin; Richard Corbett; Michelle J Tang; Ying-Chen Hou; Trevor J Pugh; Gordon Robertson; Suganthi Chittaranjan; Adrian Ally; Jennifer K Asano; Susanna Y Chan; Haiyan I Li; Helen McDonald; Kevin Teague; Yongjun Zhao; Thomas Zeng; Allen Delaney; Martin Hirst; Gregg B Morin; Steven J M Jones; Isabella T Tai; Marco A Marra Journal: Nat Methods Date: 2010-09-12 Impact factor: 28.547
Authors: Gordon Robertson; Jacqueline Schein; Readman Chiu; Richard Corbett; Matthew Field; Shaun D Jackman; Karen Mungall; Sam Lee; Hisanaga Mark Okada; Jenny Q Qian; Malachi Griffith; Anthony Raymond; Nina Thiessen; Timothee Cezard; Yaron S Butterfield; Richard Newsome; Simon K Chan; Rong She; Richard Varhol; Baljit Kamoh; Anna-Liisa Prabhu; Angela Tam; YongJun Zhao; Richard A Moore; Martin Hirst; Marco A Marra; Steven J M Jones; Pamela A Hoodless; Inanc Birol Journal: Nat Methods Date: 2010-10-10 Impact factor: 28.547
Authors: Ryan D Morin; Karen Mungall; Erin Pleasance; Andrew J Mungall; Rodrigo Goya; Ryan D Huff; David W Scott; Jiarui Ding; Andrew Roth; Readman Chiu; Richard D Corbett; Fong Chun Chan; Maria Mendez-Lago; Diane L Trinh; Madison Bolger-Munro; Greg Taylor; Alireza Hadj Khodabakhshi; Susana Ben-Neriah; Julia Pon; Barbara Meissner; Bruce Woolcock; Noushin Farnoud; Sanja Rogic; Emilia L Lim; Nathalie A Johnson; Sohrab Shah; Steven Jones; Christian Steidl; Robert Holt; Inanc Birol; Richard Moore; Joseph M Connors; Randy D Gascoyne; Marco A Marra Journal: Blood Date: 2013-05-22 Impact factor: 22.113