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. 2012 Jul 15;28(14):1919-20.
doi: 10.1093/bioinformatics/bts277. Epub 2012 May 9.

BEDOPS: high-performance genomic feature operations

Shane Neph  1 , M Scott Kuehn, Alex P Reynolds, Eric Haugen, Robert E Thurman, Audra K Johnson, Eric Rynes, Matthew T Maurano, Jeff Vierstra, Sean Thomas, Richard Sandstrom, Richard Humbert, John A Stamatoyannopoulos
Affiliations

BEDOPS: high-performance genomic feature operations

Shane Neph et al. Bioinformatics. .

Abstract

The large and growing number of genome-wide datasets highlights the need for high-performance feature analysis and data comparison methods, in addition to efficient data storage and retrieval techniques. We introduce BEDOPS, a software suite for common genomic analysis tasks which offers improved flexibility, scalability and execution time characteristics over previously published packages. The suite includes a utility to compress large inputs into a lossless format that can provide greater space savings and faster data extractions than alternatives.

Availability: http://code.google.com/p/bedops/ includes binaries, source and documentation.

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Figures

Fig. 1.
Fig. 1.
Performance results using subsets of 46-way phyloP (Pollard et al., 2010) human conservation data as inputs. (a) The time and memory resources used to merge overlapping and adjoining genomic segments as a function of input size. (b) Compressed file sizes on disk as a percentage of original uncompressed sizes. (c) Single-chromosome data extraction times from files containing >2.8×109 sorted records. BEDOPS accessed target chromosome data only, whereas conventional approaches processed inputs sequentially
See this image and copyright information in PMC

References

    1. Danacek P., et al. The variant call format and VCFtools. Bioinformatics. 2011;27:2156–2158. - PMC - PubMed
    1. Giardine B., et al. Galaxy: a platform for interactive large-scale genome analysis. Genome Res. 2005;15:1451–1455. - PMC - PubMed
    1. Kent W.J., et al. The human genome browser at UCSC. Genome Res. 2002;12:996–1006. - PMC - PubMed
    1. Li H., et al. The sequence alignment/map format and SAMtools. Bioinformatics. 2009;25:2078–2079. - PMC - PubMed
    1. Pollard K.S., et al. Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res. 2010;20:110–121. - PMC - PubMed

Publication types