A suite of tools to address common questions raised in genomic studies, mostly with regard to overlap and proximity relationships between data sets

Code: http://code.google.com/p/bedops/

Paper: http://bioinformatics.oxfordjournals.org/content/early/2012/05/09/bioinformatics.bts277.abstract

BEDOPS aims to be scalable, flexible and performant, facilitating the efficient and accurate analysis and management of large-scale genomic data