CrossMap: a versatile tool for coordinate conversion between genome assemblies

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ID: 307500
2013
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Abstract
Abstract 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 browser extensible data or general feature format, but none have the functionality to convert files in sequence alignment map or BigWig format. This is a significant gap in computational genomics tools, as these formats are the ones most widely used for representing high-throughput sequencing data, such as RNA-seq, chromatin immunoprecipitation sequencing, 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, sequence alignment map, Wiggle, BigWig, browser extensible data, general feature format, gene transfer format and variant call format. 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/. Contact: Kocher.JeanPierre@mayo.edu or wang.liguo@mayo.edu Supplementary information: Supplementary data are available at Bioinformatics online.
Reference Key
openalex_W2101071606 Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Hao Zhao, Zhifu Sun, Jing Wang, Haojie Huang, Jean‐Pierre Kocher, Liguo Wang
Journal BMC Bioinformatics
Year 2013
DOI
10.1093/bioinformatics/btt730
URL
https://academic.oup.com/bioinformatics/article-pdf/30/7/1006/17148681/btt730.pdf
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