Summary: 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.

Contact:  sjn@u.washington.edu and jstam@u.washington.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.