Ensembl Genomes Fungi data slicer

Ensembl Genomes Fungi data slicer extracts genomic subsets from BAM and VCF files to enable targeted analysis of fungal genome annotations from Ensembl.

Key Features:

• Data slicing from BAM and VCF: Extracts genomic regions and variant subsets directly from BAM and VCF files.
• Data Access and Integration: Leverages Ensembl databases, including annotations from 87 species across main and early access platforms.
• Annotation Updates: Provides access to current genome assemblies and updates for species including human, mouse, zebrafish, rat, and legacy human assembly GRCh37.
• Variant Effect Predictor (VEP) integration: Integrates VEP with additional third-party data to enhance variant consequence annotation.
• RESTful API support: Supports RESTful APIs for larger-scale and programmatic genomic analyses.
• BioMart integration: Integrates BioMart for regulatory data retrieval and high-performance queries.
• Advanced data visualization: Supports display of long-range interactions from cis-regulated datasets for analysis of genomic regulation.

Scientific Applications:

• Genomic Annotation: Enables extraction of annotated fungal genomic regions to support genome annotation and curation.
• Variant Analysis: Facilitates targeted variant analysis by extracting VCF/BAM subsets and annotating variants with VEP.
• Comparative Genomics: Provides cross-species annotated data from Ensembl to support comparative analyses across fungi and other species.
• Functional Genomics: Supports investigation of gene function and regulation, including analysis of long-range cis interactions.

Methodology:

Uses Ensembl genomic datasets; integrates with the Variant Effect Predictor (VEP) and BioMart; and exposes functionality via RESTful APIs for scalable data slicing.