Introduction

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/.

Publications

  1. CrossMap: a versatile tool for coordinate conversion between genome assemblies.
    Cite this
    Zhao H, Sun Z, Wang J, Huang H, Kocher JP, Wang L, 2014-04-01 - Bioinformatics (Oxford, England)

Credits

  1. Hao Zhao
    Developer

    Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, United States of America

  2. Zhifu Sun
    Developer

  3. Jing Wang
    Developer

  4. Haojie Huang
    Developer

  5. Jean-Pierre Kocher
    Developer

  6. Liguo Wang
    Investigator

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Summary
AccessionBT006682
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC
User InterfaceTerminal Command Line
Download Count0
Submitted ByLiguo Wang