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

Hao Zhao1, Zhifu Sun, Jing Wang

  • 1Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA, Division of Biomedical Statistics and Informatics, Mayo Clinic College of Medicine, Rochester, MN 55905, USA and Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA.

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Summary

Researchers can now convert genome files between assemblies using CrossMap. This tool supports common formats like Sequence Alignment Map and BigWig, crucial for high-throughput sequencing data analysis.

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Area of Science:

  • Genomics
  • Bioinformatics

Background:

  • Reference genome assemblies are frequently updated, necessitating data conversion for comparative analyses.
  • Existing tools lack support for essential high-throughput sequencing data formats like Sequence Alignment Map (BAM) and BigWig.

Purpose of the Study:

  • To develop a versatile and efficient tool for converting genome coordinates between different assembly versions.
  • To address the gap in computational genomics tools for handling Sequence Alignment Map and BigWig files.

Main Methods:

  • Developed CrossMap, a tool implemented in Python and C.
  • CrossMap supports conversion for multiple common genomic file formats.

Main Results:

  • CrossMap enables seamless conversion of genome coordinates across assemblies.
  • The tool supports a wide range of formats including BAM, Sequence Alignment Map, Wiggle, BigWig, BED, GFF, GTF, and VCF.

Conclusions:

  • CrossMap provides a comprehensive solution for genome assembly data conversion.
  • This tool facilitates meta-analysis, data integration, and visualization by enabling cross-assembly comparisons.