De novo transcriptome assembly with ABySS

被引：299

作者：

Birol, Inanc ^{[1
]}

Jackman, Shaun D. ^{[1
]}

Nielsen, Cydney B. ^{[1
]}

Qian, Jenny Q. ^{[1
]}

Varhol, Richard ^{[1
]}

Stazyk, Greg ^{[1
]}

Morin, Ryan D. ^{[1
]}

Zhao, Yongjun ^{[1
]}

Hirst, Martin ^{[1
]}

Schein, Jacqueline E. ^{[1
]}

Horsman, Doug E. ^{[2
]}

Connors, Joseph M. ^{[2
]}

Gascoyne, Randy D. ^{[2
]}

Marra, Marco A. ^{[1
]}

Jones, Steven J. M. ^{[1
]}

机构：

[1] Genome Sci Ctr, Vancouver, BC V5Z 4S6, Canada

[2] British Columbia Canc Agcy, Vancouver, BC V5Z 4E6, Canada

来源：

BIOINFORMATICS | 2009年 / 25卷 / 21期

关键词：

D O I：

10.1093/bioinformatics/btp367

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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 similar to 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.

引用

页码：2872 / 2877

页数：6

共 25 条

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