Ensembl Genomes Plants data slicer

Ensembl Genomes Plants Data Slicer extracts subsets of genomic data from BAM and VCF files and retrieves Ensembl annotations to support plant genomic and variant analyses.

Key Features:

• Data Extraction: Retrieves targeted subsets of reads and variants from BAM and VCF files for specific genomic regions or loci.
• Integration with Ensembl Resources: Leverages Ensembl genomic data and annotations across 87 species, including human, mouse, zebrafish, and rat.
• Enhanced Analysis Tools: Integrates Variant Effect Predictor (VEP) with additional third-party data to provide expanded variant effect predictions.
• Scalability and Performance: Uses RESTful APIs for large-scale data access and incorporates BioMart regulatory data service optimizations for faster result delivery.
• Visualization of Regulatory Interactions: Provides representation of long-range interactions within cis-regulated datasets to support regulatory analysis.

Scientific Applications:

• Genomic Research: Enables precise extraction and annotation of genomic regions to support comparative and functional studies in plants.
• Variant Analysis: Supports identification and characterization of genetic variants within defined regions using VEP annotations.
• Regulatory Studies: Assists exploration of regulatory elements and long-range cis-regulatory interactions using BioMart and interaction visualizations.

Methodology:

Interfaces with Ensembl databases and utilizes RESTful APIs for data access and manipulation; supports integration with other bioinformatics tools and workflows.