Hadoop-BAM: directly manipulating next generation sequencing data in the cloud

被引：84

作者：

Niemenmaa, Matti ^{[1
]}

Kallio, Aleksi ^{[2
]}

Schumacher, Andre ^{[1
]}

Klemela, Petri ^{[2
]}

Korpelainen, Eija ^{[2
]}

Heljanko, Keijo ^{[1
]}

机构：

[1] Aalto Univ, Dept Informat & Comp Sci, FI-00076 Aalto, Finland

[2] CSC IT Ctr Sci Ltd, FI-02101 Espoo, Finland

来源：

BIOINFORMATICS | 2012年 / 28卷 / 06期

基金：

芬兰科学院;

关键词：

FRAMEWORK; MAPREDUCE;

D O I：

10.1093/bioinformatics/bts054

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Hadoop-BAM is a novel library for the scalable manipulation of aligned next-generation sequencing data in the Hadoop distributed computing framework. It acts as an integration layer between analysis applications and BAM files that are processed using Hadoop. Hadoop-BAM solves the issues related to BAM data access by presenting a convenient API for implementing map and reduce functions that can directly operate on BAM records. It builds on top of the Picard SAM JDK, so tools that rely on the Picard API are expected to be easily convertible to support large-scale distributed processing. In this article we demonstrate the use of Hadoop-BAM by building a coverage summarizing tool for the Chipster genome browser. Our results show that Hadoop offers good scalability, and one should avoid moving data in and out of Hadoop between analysis steps.

引用

页码：876 / 877

页数：2

共 10 条

[1]

[Anonymous], 2009, Hadoop: The Definitive Guide

[2]

Dean J, 2004, USENIX ASSOCIATION PROCEEDINGS OF THE SIXTH SYMPOSIUM ON OPERATING SYSTEMS DESIGN AND IMPLEMENTATION (OSDE '04), P137

[3] Chipster: user-friendly analysis software for microarray and other high-throughput data [J].

Kallio, M. Aleksi ;

Tuimala, Jarno T. ;

Hupponen, Taavi ;

Klemela, Petri ;

Gentile, Massimiliano ;

Scheinin, Ilari ;

Koski, Mikko ;

Kaki, Janne ;

Korpelainen, Eija I. .

BMC GENOMICS, 2011, 12

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

Li, Heng ;

Durbin, Richard .

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

[5] 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

[6] SeqWare Query Engine: storing and searching sequence data in the cloud [J].

O'Connor, Brian D. ;

Merriman, Barry ;

Nelson, Stanley F. .

BMC BIOINFORMATICS, 2010, 11

[7]

Olston C., 2008, Proceedings of the 2008 ACM SIGMOD international conference on Management Of Data, SIGMOD '08, P1099

[8] SEAL: a distributed short read mapping and duplicate removal tool [J].

Pireddu, Luca ;

Leo, Simone ;

Zanetti, Gianluigi .

BIOINFORMATICS, 2011, 27 (15) :2159-2160

[9] An overview of the Hadoop/MapReduce/HBase framework and its current applications in bioinformatics [J].

Taylor, Ronald C. .

BMC BIOINFORMATICS, 2010, 11

[10] Hive - A Petabyte Scale Data Warehouse Using Hadoop [J].

Thusoo, Ashish ;

Sen Sarma, Joydeep ;

Jain, Namit ;

Shao, Zheng ;

Chakka, Prasad ;

Zhang, Ning ;

Antony, Suresh ;

Liu, Hao ;

Murthy, Raghotham .

26TH INTERNATIONAL CONFERENCE ON DATA ENGINEERING ICDE 2010, 2010, :996-1005

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