De novo assembly and analysis of RNA-seq data

被引：638

作者：

Robertson, Gordon ^{[1
]}

Schein, Jacqueline ^{[1
]}

Chiu, Readman ^{[1
]}

Corbett, Richard ^{[1
]}

Field, Matthew ^{[1
]}

Jackman, Shaun D. ^{[1
]}

Mungall, Karen ^{[1
]}

Lee, Sam ^{[2
]}

Okada, Hisanaga Mark ^{[1
]}

Qian, Jenny Q. ^{[1
]}

Griffith, Malachi ^{[1
]}

Raymond, Anthony ^{[1
]}

Thiessen, Nina ^{[1
]}

Cezard, Timothee ^{[1
]}

Butterfield, Yaron S. ^{[1
]}

Newsome, Richard ^{[1
]}

Chan, Simon K. ^{[1
]}

She, Rong ^{[1
]}

Varhol, Richard ^{[1
]}

Kamoh, Baljit ^{[1
]}

Prabhu, Anna-Liisa ^{[1
]}

Tam, Angela ^{[1
]}

Zhao, YongJun ^{[1
]}

Moore, Richard A. ^{[1
]}

Hirst, Martin ^{[1
]}

Marra, Marco A. ^{[1
,3
]}

Jones, Steven J. M. ^{[1
,3
]}

Hoodless, Pamela A. ^{[2
,3
]}

Birol, Inanc ^{[1
]}

机构：

[1] British Columbia Canc Agcy, Canadas Michael Smith Genome Sci Ctr, Vancouver, BC V5Z 4E6, Canada

[2] British Columbia Canc Agcy, Terry Fox Lab, Vancouver, BC V5Z 1L3, Canada

[3] Univ British Columbia, Dept Med Genet, Vancouver, BC, Canada

来源：

NATURE METHODS | 2010年 / 7卷 / 11期

关键词：

SPLICE JUNCTIONS; EXPRESSION; ALIGNMENT; TRANSCRIPTS; GENERATION; REVEALS; GENOMES; READS; RATES;

D O I：

10.1038/nmeth.1517

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

We describe Trans-ABySS, a de novo short-read transcriptome assembly and analysis pipeline that addresses variation in local read densities by assembling read substrings with varying stringencies and then merging the resulting contigs before analysis. Analyzing 7.4 gigabases of 50-base-pair paired-end Illumina reads from an adult mouse liver poly(A) RNA library, we identified known, new and alternative structures in expressed transcripts, and achieved high sensitivity and specificity relative to reference-based assembly methods.

引用

页码：909 / U62

页数：7

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