Universität zu Köln

Wittelsbuerger, Ulrich, Pfeifer, Bastian ORCID: 0000-0001-7035-9535 and Lercher, Martin J. (2015). WhopGenome: high-speed access to whole-genome variation and sequence data in R. Bioinformatics, 31 (3). S. 413 - 416. OXFORD: OXFORD UNIV PRESS. ISSN 1460-2059

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Abstract

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.

Item Type:	Journal Article
Creators:	Creators Email ORCID ORCID Put Code Wittelsbuerger, Ulrich UNSPECIFIED UNSPECIFIED UNSPECIFIED Pfeifer, Bastian UNSPECIFIED orcid.org/0000-0001-7035-9535 UNSPECIFIED Lercher, Martin J. UNSPECIFIED UNSPECIFIED UNSPECIFIED
URN:	urn:nbn:de:hbz:38-413065
DOI:	10.1093/bioinformatics/btu636
Journal or Publication Title:	Bioinformatics
Volume:	31
Number:	3
Page Range:	S. 413 - 416
Date:	2015
Publisher:	OXFORD UNIV PRESS
Place of Publication:	OXFORD
ISSN:	1460-2059
Language:	English
Faculty:	Unspecified
Divisions:	Unspecified
Subjects:	no entry
Uncontrolled Keywords:	Keywords Language BIOCONDUCTOR; ANNOTATION; FORMAT Multiple languages Biochemical Research Methods; Biotechnology & Applied Microbiology; Computer Science, Interdisciplinary Applications; Mathematical & Computational Biology; Statistics & Probability Multiple languages
URI:	http://kups.ub.uni-koeln.de/id/eprint/41306