Assembly converter

Assembly converter maps genomic coordinates, annotations, and associated data between genome assemblies to enable cross-assembly comparison and dataset integration.

Key Features:

• Cross-Assembly Mapping: Enables mapping of genomic coordinates and annotations between current and previous genome assemblies to support continuity of analyses.
• Integration with Ensembl Resources: Leverages Ensembl databases covering 87 species, including human, mouse, zebrafish, and rat, to provide up-to-date annotations and analyses.
• Support for Latest Genome Assemblies: Prioritizes mapping to the latest reference assemblies to facilitate analyses on current genomic sequences.
• Backward Compatibility: Provides mapping to previous assembly versions, including GRCh37 for human, to support validation of historical data and reproducibility.
• Integration with Third-Party Data: Incorporates third-party datasets into the mapping process to enhance annotation coverage and accuracy.
• Scalability and Performance Enhancements: Supports large-scale analyses with improvements in REST capabilities and optimized regulatory data access via BioMart.
• Visualization of Long-Range Interactions: Supports visualization of long-range genomic interactions, including those found in cis-regulated datasets.

Scientific Applications:

• Comparative Genomics: Enables comparison of genomes and annotations across species and assembly versions.
• Variant Analysis: Maps genetic variants to current assemblies for accurate variant interpretation.
• Regulatory Studies: Facilitates exploration of regulatory elements and their long-range interactions.
• Data Integration: Enables integration of diverse datasets into a common assembly framework for combined analyses.

Methodology:

Implements algorithms for precise mapping between genome assemblies while leveraging Ensembl's comprehensive databases, integrating third-party data, and using REST improvements and BioMart-optimized regulatory data access.