SeqPig: simple and scalable scripting for large sequencing data sets in Hadoop.
Bioinformatics
; 30(1): 119-20, 2014 Jan 01.
Article
em En
| MEDLINE
| ID: mdl-24149054
ABSTRACT
SUMMARY:
Hadoop MapReduce-based approaches have become increasingly popular due to their scalability in processing large sequencing datasets. However, as these methods typically require in-depth expertise in Hadoop and Java, they are still out of reach of many bioinformaticians. To solve this problem, we have created SeqPig, a library and a collection of tools to manipulate, analyze and query sequencing datasets in a scalable and simple manner. SeqPigscripts use the Hadoop-based distributed scripting engine Apache Pig, which automatically parallelizes and distributes data processing tasks. We demonstrate SeqPig's scalability over many computing nodes and illustrate its use with example scripts. AVAILABILITY AND IMPLEMENTATION Available under the open source MIT license at http//sourceforge.net/projects/seqpig/
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Design de Software
/
Ensaios de Triagem em Larga Escala
Idioma:
En
Revista:
Bioinformatics
Assunto da revista:
INFORMATICA MEDICA
Ano de publicação:
2014
Tipo de documento:
Article
País de afiliação:
Finlândia