Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 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.

PubMed Disclaimer

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

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

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