Tuesday, January 7, 2014

Fwd: CrossMap: a versatile tool for coordinate conversion between genome assemblies

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CrossMap: a versatile tool for coordinate conversion between genome assemblies: "

Motivation: Reference genome assemblies are subject to change and refinement from time to time. Generally, researchers need to convert the results that have been analyzed according to old assemblies to newer versions, or vice versa, to facilitate meta-analysis, direct comparison, data integration, and visualization. Several useful conversion tools can convert genome interval files in BED or GFF format, but none have the functionality to convert files in BAM/SAM or BigWig format. This is a significant gap in computational genomics tools, since these formats are the ones most widely used for representing high-throughput sequencing data, such as RNA-seq, ChIP-seq, DNA-seq, etc.

Results: Here we developed CrossMap, a versatile and efficient tool for converting genome coordinates between assemblies. CrossMap supports most of the commonly used file formats, including BAM, SAM, Wiggle, BigWig, BED, GFF, GTF, and VCF.

Availability and implementation: CrossMap is written in Python and C. Source code and a comprehensive user's manual are freely available at: http://crossmap.sourceforge.net/.

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(Via Bioinformatics - Advance Access.)