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
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
收藏
页码:284 / 285
页数:2
相关论文
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