De novo transcriptome assembly with ABySS

被引：302

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

[1] Accurate whole human genome sequencing using reversible terminator chemistry [J].

Bentley, David R. ;

Balasubramanian, Shankar ;

Swerdlow, Harold P. ;

Smith, Geoffrey P. ;

Milton, John ;

Brown, Clive G. ;

Hall, Kevin P. ;

Evers, Dirk J. ;

Barnes, Colin L. ;

Bignell, Helen R. ;

Boutell, Jonathan M. ;

Bryant, Jason ;

Carter, Richard J. ;

Cheetham, R. Keira ;

Cox, Anthony J. ;

Ellis, Darren J. ;

Flatbush, Michael R. ;

Gormley, Niall A. ;

Humphray, Sean J. ;

Irving, Leslie J. ;

Karbelashvili, Mirian S. ;

Kirk, Scott M. ;

Li, Heng ;

Liu, Xiaohai ;

Maisinger, Klaus S. ;

Murray, Lisa J. ;

Obradovic, Bojan ;

Ost, Tobias ;

Parkinson, Michael L. ;

Pratt, Mark R. ;

Rasolonjatovo, Isabelle M. J. ;

Reed, Mark T. ;

Rigatti, Roberto ;

Rodighiero, Chiara ;

Ross, Mark T. ;

Sabot, Andrea ;

Sankar, Subramanian V. ;

Scally, Aylwyn ;

Schroth, Gary P. ;

Smith, Mark E. ;

Smith, Vincent P. ;

Spiridou, Anastassia ;

Torrance, Peta E. ;

Tzonev, Svilen S. ;

Vermaas, Eric H. ;

Walter, Klaudia ;

Wu, Xiaolin ;

Zhang, Lu ;

Alam, Mohammed D. ;

Anastasi, Carole .

NATURE, 2008, 456 (7218) :53-59

[2] ALLPATHS: De novo assembly of whole-genome shotgun microreads [J].

Butler, Jonathan ;

MacCallum, Iain ;

Kleber, Michael ;

Shlyakhter, Ilya A. ;

Belmonte, Matthew K. ;

Lander, Eric S. ;

Nusbaum, Chad ;

Jaffe, David B. .

GENOME RESEARCH, 2008, 18 (05) :810-820

[3] Short read fragment assembly of bacterial genomes [J].

Chaisson, Mark J. ;

Pevzner, Pavel A. .

GENOME RESEARCH, 2008, 18 (02) :324-330

[4]

de Bruijn N G., 1946, Proc. Sec. Sci. K. Ned. Akad. Wet. te Amsterdam, V49, P758

[5] SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing [J].

Dohm, Juliane C. ;

Lottaz, Claudio ;

Borodina, Tatiana ;

Himmelbauer, Heinz .

GENOME RESEARCH, 2007, 17 (11) :1697-1706

[6] De novo assembly of the Pseudomonas syringae pv. syringae B728a genome using Illumina/Solexa short sequence reads [J].

Farrer, Rhys A. ;

Kemen, Eric ;

Jones, Jonathan D. G. ;

Studholme, David J. .

FEMS MICROBIOLOGY LETTERS, 2009, 291 (01) :103-111

[7] Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses [J].

Fullwood, Melissa J. ;

Wei, Chia-Lin ;

Liu, Edison T. ;

Ruan, Yijun .

GENOME RESEARCH, 2009, 19 (04) :521-532

[8] De novo bacterial genome sequencing: Millions of very short reads assembled on a desktop computer [J].

Hernandez, David ;

Francois, Patrice ;

Farinelli, Laurent ;

Osteras, Magne ;

Schrenzel, Jacques .

GENOME RESEARCH, 2008, 18 (05) :802-809

[9] The UCSC Known Genes [J].

Hsu, F ;

Kent, WJ ;

Clawson, H ;

Kuhn, RM ;

Diekhans, M ;

Haussler, D .

BIOINFORMATICS, 2006, 22 (09) :1036-1046

[10] Parallel short sequence assembly of transcriptomes [J].

Jackson, Benjamin G. ;

Schnable, Patrick S. ;

Aluru, Srinivas .

BMC BIOINFORMATICS, 2009, 10

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