Name
Abstract | ||
|---|---|---|
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.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.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.ibirol@bcgsc.ca. |
Year | DOI | Venue |
|---|---|---|
2009 | 10.1093/bioinformatics/btp367 | Bioinformatics |
Keywords | Field | DocType |
base pair,novel event,assembler tool,million base pair,java universal network,abyss-explorer tool,unique opportunity,unique transcriptome sequence,sequence coverage,novel isoforms | Genome,Shotgun sequencing,De novo transcriptome assembly,Biology,Transcriptome,Contig,Bioinformatics,Java,Base pair,Sequence assembly | Journal |
Volume | Issue | ISSN |
25 | 21 | 1367-4811 |
Citations | PageRank | References |
33 | 3.05 | 6 |
Authors | ||
15 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| İnanç Birol | 1 | 97 | 8.16 |
| Shaun D Jackman | 2 | 72 | 7.37 |
| Cydney B Nielsen | 3 | 55 | 4.78 |
| Jenny Q Qian | 4 | 33 | 3.05 |
| Richard Varhol | 5 | 106 | 13.43 |
| Greg Stazyk | 6 | 33 | 3.05 |
| Ryan Morin | 7 | 106 | 9.37 |
| Yongjun Zhao | 8 | 33 | 3.05 |
| Martin Hirst | 9 | 162 | 13.02 |
| Jacqueline E Schein | 10 | 39 | 3.82 |
| Doug E Horsman | 11 | 33 | 3.05 |
| Joseph M Connors | 12 | 33 | 3.05 |
| Randy D. Gascoyne | 13 | 38 | 3.57 |
| Marco A. Marra | 14 | 245 | 17.87 |
| Steven J. M. Jones | 15 | 578 | 71.55 |