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Bioinformatics. 2015 Feb 1;31(3):413-5. doi: 10.1093/bioinformatics/btu636. Epub 2014 Oct 1.

WhopGenome: high-speed access to whole-genome variation and sequence data in R.

Author information

1
Institute for Computer Science, Heinrich Heine University, D-40255 Düsseldorf, Germany and Cluster of Excellence on Plant Sciences CEPLAS, D-40255 Düsseldorf, Germany.
2
Institute for Computer Science, Heinrich Heine University, D-40255 Düsseldorf, Germany and Cluster of Excellence on Plant Sciences CEPLAS, D-40255 Düsseldorf, Germany Institute for Computer Science, Heinrich Heine University, D-40255 Düsseldorf, Germany and Cluster of Excellence on Plant Sciences CEPLAS, D-40255 Düsseldorf, Germany.

Abstract

SUMMARY:

The statistical programming language R has become a de facto standard for the analysis of many types of biological data, and is well suited for the rapid development of new algorithms. However, variant call data from population-scale resequencing projects are typically too large to be read and processed efficiently with R's built-in I/O capabilities. WhopGenome can efficiently read whole-genome variation data stored in the widely used variant call format (VCF) file format into several R data types. VCF files can be accessed either on local hard drives or on remote servers. WhopGenome can associate variants with annotations such as those available from the UCSC genome browser, and can accelerate the reading process by filtering loci according to user-defined criteria. WhopGenome can also read other Tabix-indexed files and create indices to allow fast selective access to FASTA-formatted sequence files.

AVAILABILITY AND IMPLEMENTATION:

The WhopGenome R package is available on CRAN at http://cran.r-project.org/web/packages/WhopGenome/. A Bioconductor package has been submitted.

CONTACT:

lercher@cs.uni-duesseldorf.de.

PMID:
25273104
DOI:
10.1093/bioinformatics/btu636
[Indexed for MEDLINE]

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