ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data

被引：393

作者：

Morgan, Martin ^{[1
]}

Anders, Simon ^{[2
]}

Lawrence, Michael ^{[1
]}

Aboyoun, Patrick ^{[1
]}

Pages, Herve ^{[1
]}

Gentleman, Robert ^{[1
]}

机构：

[1] Fred Hutchinson Canc Res Ctr, Program Computat Biol, Seattle, WA 98104 USA

[2] EMBL EBI, Cambridge, England

来源：

BIOINFORMATICS | 2009年 / 25卷 / 19期

关键词：

HUMAN GENOME; SEQ;

D O I：

10.1093/bioinformatics/btp450

中图分类号：

Q5 [生物化学];

学科分类号：

070307 [化学生物学];

摘要：

ShortRead is a package for input, quality assessment, manipulation and output of high-throughput sequencing data. ShortRead is provided in the R and Bioconductor environments, allowing ready access to additional facilities for advanced statistical analysis, data transformation, visualization and integration with diverse genomic resources.

引用

页码：2607 / 2608

页数：2

共 9 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]

Bioconductor: open software development for computational biology and bioinformatics [J].

Gentleman, RC ;

Carey, VJ ;

Bates, DM ;

Bolstad, B ;

Dettling, M ;

Dudoit, S ;

Ellis, B ;

Gautier, L ;

Ge, YC ;

Gentry, J ;

Hornik, K ;

Hothorn, T ;

Huber, W ;

Iacus, S ;

Irizarry, R ;

Leisch, F ;

Li, C ;

Maechler, M ;

Rossini, AJ ;

Sawitzki, G ;

Smith, C ;

Smyth, G ;

Tierney, L ;

Yang, JYH ;

Zhang, JH .

GENOME BIOLOGY, 2004, 5 (10)

[3]

Design and analysis of ChIP-seq experiments for DNA-binding proteins [J].

Kharchenko, Peter V. ;

Tolstorukov, Michael Y. ;

Park, Peter J. .

NATURE BIOTECHNOLOGY, 2008, 26 (12) :1351-1359

[4]

KUHN RM, 1955, NUCLEIC ACIDS RES, V37, pD755

[5]

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome [J].

Langmead, Ben ;

Trapnell, Cole ;

Pop, Mihai ;

Salzberg, Steven L. .

GENOME BIOLOGY, 2009, 10 (03)

[6]

Mapping short DNA sequencing reads and calling variants using mapping quality scores [J].

Li, Heng ;

Ruan, Jue ;

Durbin, Richard .

GENOME RESEARCH, 2008, 18 (11) :1851-1858

[7]

ChIP-seq: welcome to the new frontier [J].

Mardis, Elaine R. .

NATURE METHODS, 2007, 4 (08) :613-614

[8]

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

[9]

Gene expression profiling by massively parallel sequencing [J].

Torres, Tatiana Teixeira ;

Metta, Muralidhar ;

Ottenwalder, Birgit ;

Schlotterer, Christian .

GENOME RESEARCH, 2008, 18 (01) :172-177

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