Near-optimal probabilistic RNA-seq quantification

被引：2029

作者：

Bray, Nicolas L. ^{[1
]}

Pimentel, Harold ^{[2
]}

Melsted, Pall ^{[3
]}

Pachter, Lior ^{[2
,4
,5
]}

机构：

[1] Univ Calif Berkeley, Innovat Genom Initiat, Berkeley, CA 94720 USA

[2] Univ Calif Berkeley, Dept Comp Sci, Berkeley, CA 94720 USA

[3] Univ Iceland, Fac Ind Engn Mech Engn & Comp Sci, Reykjavik, Iceland

[4] Univ Calif Berkeley, Dept Math, Berkeley, CA 94720 USA

[5] Univ Calif Berkeley, Dept Mol & Cell Biol, 229 Stanley Hall, Berkeley, CA 94720 USA

来源：

NATURE BIOTECHNOLOGY | 2016年 / 34卷 / 05期

关键词：

GENOME; TRANSCRIPTOMES;

D O I：

10.1038/nbt.3519

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

We present kallisto, an RNA-seq quantification program that is two orders of magnitude faster than previous approaches and achieves similar accuracy. Kallisto pseudoaligns reads to a reference, producing a list of transcripts that are compatible with each read while avoiding alignment of individual bases. We use kallisto to analyze 30 million unaligned paired-end RNA-seq reads in <10 min on a standard laptop computer. This removes a major computational bottleneck in RNA-seq analysis.

引用

页码：525 / 527

页数：3

共 14 条

[1] HTSeq-a Python']Python framework to work with high-throughput sequencing data [J].

Anders, Simon ;

Pyl, Paul Theodor ;

Huber, Wolfgang .

BIOINFORMATICS, 2015, 31 (02) :166-169

[2] How to apply de Bruijn graphs to genome assembly [J].

Compeau, Phillip E. C. ;

Pevzner, Pavel A. ;

Tesler, Glenn .

NATURE BIOTECHNOLOGY, 2011, 29 (11) :987-991

[3] TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions [J].

Kim, Daehwan ;

Pertea, Geo ;

Trapnell, Cole ;

Pimentel, Harold ;

Kelley, Ryan ;

Salzberg, Steven L. .

GENOME BIOLOGY, 2013, 14 (04)

[4] Transcriptome and genome sequencing uncovers functional variation in humans [J].

Lappalainen, Tuuli ;

Sammeth, Michael ;

Friedlaender, Marc R. ;

't Hoen, Peter A. C. ;

Monlong, Jean ;

Rivas, Manuel A. ;

Gonzalez-Porta, Mar ;

Kurbatova, Natalja ;

Griebel, Thasso ;

Ferreira, Pedro G. ;

Barann, Matthias ;

Wieland, Thomas ;

Greger, Liliana ;

van Iterson, Maarten ;

Almloef, Jonas ;

Ribeca, Paolo ;

Pulyakhina, Irina ;

Esser, Daniela ;

Giger, Thomas ;

Tikhonov, Andrew ;

Sultan, Marc ;

Bertier, Gabrielle ;

MacArthur, Daniel G. ;

Lek, Monkol ;

Lizano, Esther ;

Buermans, Henk P. J. ;

Padioleau, Ismael ;

Schwarzmayr, Thomas ;

Karlberg, Olof ;

Ongen, Halit ;

Kilpinen, Helena ;

Beltran, Sergi ;

Gut, Marta ;

Kahlem, Katja ;

Amstislavskiy, Vyacheslav ;

Stegle, Oliver ;

Pirinen, Matti ;

Montgomery, Stephen B. ;

Donnelly, Peter ;

McCarthy, Mark I. ;

Flicek, Paul ;

Strom, Tim M. ;

Lehrach, Hans ;

Schreiber, Stefan ;

Sudbrak, Ralf ;

Carracedo, Angel ;

Antonarakis, Stylianos E. ;

Haesler, Robert ;

Syvaenen, Ann-Christine ;

Van Ommen, Gert-Jan .

NATURE, 2013, 501 (7468) :506-511

[5] RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome [J].

Li, Bo ;

Dewey, Colin N. .

BMC BIOINFORMATICS, 2011, 12

[6]

Marconi J. C., 2008, GENOME RES, V18, P1509

[7] Mapping and quantifying mammalian transcriptomes by RNA-Seq [J].

Mortazavi, Ali ;

Williams, Brian A. ;

McCue, Kenneth ;

Schaeffer, Lorian ;

Wold, Barbara .

NATURE METHODS, 2008, 5 (07) :621-628

[8]

Nicolae M, 2010, LECT N BIOINFORMAT, V6293, P202, DOI 10.1007/978-3-642-15294-8_17

[9] Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms [J].

Patro, Rob ;

Mount, Stephen M. ;

Kingsford, Carl .

NATURE BIOTECHNOLOGY, 2014, 32 (05) :462-U174

[10]

Roberts A, 2013, NAT METHODS, V10, P71, DOI [10.1038/NMETH.2251, 10.1038/nmeth.2251]

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