Ensembl Genomes Protists data slicer

Ensembl Genomes Protists data slicer extracts subsets of genomic data (BAM, VCF) and associated Ensembl Genomes annotations to support analysis of protist genomes and comparative studies across species.

Key Features:

• Data Access and Annotation: Provides access to genomic data and up-to-date genome assemblies and annotations across 87 species, with a stated focus on chordates and key model organisms.
• Integration of Third-Party Data: Incorporates additional third-party datasets and supports integration with the Variant Effect Predictor (VEP) for enriched variant annotation.
• Scalability and Performance: Supports large-scale genomic analyses via the REST API and offers fast access to regulatory data through BioMart.
• Visualization of Long-Range Interactions: Enables visualization of long-range interactions within cis-regulated datasets to support analysis of gene regulation mechanisms.

Scientific Applications:

• Targeted data extraction: Extract specific data subsets from large-scale BAM and VCF files for region-focused analyses.
• Variant effect analysis: Analyze genetic variation and predicted effects using integrated third-party datasets and the Variant Effect Predictor (VEP).
• Regulatory and interaction studies: Investigate regulatory elements and long-range cis interactions within protist genomes.
• Comparative genomics: Access comprehensive annotations across multiple species to facilitate comparative genomics investigations.

Methodology:

Leverages the Ensembl infrastructure, performs slicing of BAM and VCF files to extract regions of interest, and integrates the REST API and BioMart for large-scale programmatic access to annotated genomic data.