Extending KNIME for next-generation sequencing data analysis

被引：27

作者：

Jagla, Bernd ^{[1
]}

Wiswedel, Bernd ^{[2
]}

Coppee, Jean-Yves ^{[1
]}

机构：

[1] Inst Pasteur, Dept Genomes & Genet, F-75015 Paris, France

[2] KNIME Com AG, CH-8005 Zurich, Switzerland

来源：

BIOINFORMATICS | 2011年 / 27卷 / 20期

关键词：

D O I：

10.1093/bioinformatics/btr478

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

KNIME (Konstanz Information Miner) is a user-friendly and comprehensive open-source data integration, processing, analysis and exploration platform. We present here new functionality and workflows that open the door to performing next-generation sequencing analysis using the KNIME framework.

引用

页码：2907 / 2909

页数：3

共 12 条

[1] KNIME:: The Konstanz Information Miner [J].

Berthold, Michael R. ;

Cebron, Nicolas ;

Dill, Fabian ;

Gabriel, Thomas R. ;

Koetter, Tobias ;

Meinl, Thorsten ;

Ohl, Peter ;

Sieb, Christoph ;

Thiel, Kilian ;

Wiswedel, Bernd .

DATA ANALYSIS, MACHINE LEARNING AND APPLICATIONS, 2008, :319-326

[2] geWorkbench: an open source platform for integrative genomics [J].

Floratos, Aris ;

Smith, Kenneth ;

Ji, Zhou ;

Watkinson, John ;

Califano, Andrea .

BIOINFORMATICS, 2010, 26 (14) :1779-1780

[3] myExperiment: a repository and social network for the sharing of bioinformatics workflows [J].

Goble, Carole A. ;

Bhagat, Jiten ;

Aleksejevs, Sergejs ;

Cruickshank, Don ;

Michaelides, Danius ;

Newman, David ;

Borkum, Mark ;

Bechhofer, Sean ;

Roos, Marco ;

Li, Peter ;

De Roure, David .

NUCLEIC ACIDS RESEARCH, 2010, 38 :W677-W682

[4] Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences [J].

Goecks, Jeremy ;

Nekrutenko, Anton ;

Taylor, James .

GENOME BIOLOGY, 2010, 11 (08)

[5] Taverna: a tool for building and running workflows of services [J].

Hull, Duncan ;

Wolstencroft, Katy ;

Stevens, Robert ;

Goble, Carole ;

Pocock, Mathew R. ;

Li, Peter ;

Oinn, Tom .

NUCLEIC ACIDS RESEARCH, 2006, 34 :W729-W732

[6] The human genome browser at UCSC [J].

Kent, WJ ;

Sugnet, CW ;

Furey, TS ;

Roskin, KM ;

Pringle, TH ;

Zahler, AM ;

Haussler, D .

GENOME RESEARCH, 2002, 12 (06) :996-1006

[7] Fast and accurate short read alignment with Burrows-Wheeler transform [J].

Li, Heng ;

Durbin, Richard .

BIOINFORMATICS, 2009, 25 (14) :1754-1760

[8] Conveyor: a workflow engine for bioinformatic analyses [J].

Linke, Burkhard ;

Giegerich, Robert ;

Goesmann, Alexander .

BIOINFORMATICS, 2011, 27 (07) :903-911

[9] Scientific workflow management and the Kepler system [J].

Ludascher, Bertram ;

Altintas, Ilkay ;

Berkley, Chad ;

Higgins, Dan ;

Jaeger, Efrat ;

Jones, Matthew ;

Lee, Edward A. ;

Tao, Jing ;

Zhao, Yang .

CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE, 2006, 18 (10) :1039-1065

[10] Mobyle: a new full web bioinformatics framework [J].

Neron, Bertrand ;

Menager, Herve ;

Maufrais, Corinne ;

Joly, Nicolas ;

Maupetit, Julien ;

Letort, Sebastien ;

Carrere, Sebastien ;

Tuffery, Pierre ;

Letondal, Catherine .

BIOINFORMATICS, 2009, 25 (22) :3005-3011

← 1 2 →