NARWHAL, a primary analysis pipeline for NGS data

被引：32

作者：

Brouwer, R. W. W. ^{[1
,2
]}

van den Hout, M. C. G. N. ^{[1
]}

Grosveld, F. G. ^{[1
]}

van IJcken, W. F. J. ^{[1
]}

机构：

[1] Erasmus MC, Ctr Biom, Dept Cell Biol, Rotterdam, Netherlands

[2] Netherlands Bioinformat Ctr NBIC, Nijmegen, Netherlands

来源：

BIOINFORMATICS | 2012年 / 28卷 / 02期

关键词：

GENOME ANALYSIS; ALIGNMENT; SEQUENCE;

D O I：

10.1093/bioinformatics/btr613

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

The NARWHAL software pipeline has been developed to automate the primary analysis of Illumina sequencing data. This pipeline combines a new and flexible de-multiplexing tool with open-source aligners and automated quality assessment. The entire pipeline can be run using only one simple sample-sheet for diverse sequencing applications. NARWHAL creates a sample-oriented data structure and outperforms existing tools in speed.

引用

页码：284 / 285

页数：2

共 6 条

[1] ngs_backbone: a pipeline for read cleaning, mapping and SNP calling using Next Generation Sequence [J].

Blanca, Jose M. ;

Pascual, Laura ;

Ziarsolo, Peio ;

Nuez, Fernando ;

Canizares, Joaquin .

BMC GENOMICS, 2011, 12

[2] Galaxy: A platform for interactive large-scale genome analysis [J].

Giardine, B ;

Riemer, C ;

Hardison, RC ;

Burhans, R ;

Elnitski, L ;

Shah, P ;

Zhang, Y ;

Blankenberg, D ;

Albert, I ;

Taylor, J ;

Miller, W ;

Kent, WJ ;

Nekrutenko, A .

GENOME RESEARCH, 2005, 15 (10) :1451-1455

[3] Genome-wide mapping of in vivo protein-DNA interactions [J].

Johnson, David S. ;

Mortazavi, Ali ;

Myers, Richard M. ;

Wold, Barbara .

SCIENCE, 2007, 316 (5830) :1497-1502

[4] 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)

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

Li, Heng ;

Durbin, Richard .

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

[6] The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data [J].

McKenna, Aaron ;

Hanna, Matthew ;

Banks, Eric ;

Sivachenko, Andrey ;

Cibulskis, Kristian ;

Kernytsky, Andrew ;

Garimella, Kiran ;

Altshuler, David ;

Gabriel, Stacey ;

Daly, Mark ;

DePristo, Mark A. .

GENOME RESEARCH, 2010, 20 (09) :1297-1303

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