ENCODE Software
Software tools used in integrative analysis for the development of the Encyclopedia and SCREEN
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- bedToBigBed — sourcebedToBigBed takes a standard bed file or a non-standard bed file with associated .as file to create a compressed bigBed version. Description of Big Binary Indexed (BBI) files and visualization of next-generation sequencing experiment results explained by W.J. Kent, PMCID: PMC2922891.Software type: file format conversion
- BEDTools — sourceCollectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetics: that is, set theory on the genome. For example, bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, and VCF.Software type: file format conversion