CrossMap

CrossMap converts genome coordinates between different reference assemblies to enable comparison, integration, and meta-analysis of genomic datasets.

Key Features:

• Coordinate conversion: Converts genome coordinates between different reference assemblies.
• File format support: Transforms files in formats including BAM, SAM, WIG, BigWig, BED, GFF, GTF, and VCF.
• Sequencing data compatibility: Applicable to high-throughput sequencing data types such as RNA-seq, ChIP-seq, and DNA-seq.
• Implementation: Implemented in Python and C.

Scientific Applications:

• Meta-analysis: Facilitates meta-analysis by harmonizing coordinates from studies using different reference assemblies.
• Comparative analysis: Enables direct comparison of genomic features across assembly versions.
• Data integration: Supports integration of datasets produced on different reference assemblies for combined analyses.
• Visualization: Prepares sequence alignments, coverage tracks, annotations, and variant calls for visualization across assemblies.

Methodology:

Performs coordinate conversion of BAM, SAM, WIG, BigWig, BED, GFF, GTF, and VCF files and is implemented in Python and C.