clc_find_variations_tab_convertor

clc_find_variations_tab_convertor converts CLC Genomics Workbench find_variations output into a tabular format compatible with snpEff to enable functional annotation of genomic variants.

Key Features:

• Format Conversion: Converts CLC Genomics Workbench find_variations output into a snpEff-compatible tab-delimited format for downstream functional annotation.
• Galaxy Integration: Executes on the Galaxy@Pasteur instance and can run on the Institut Pasteur cluster to leverage workflow execution on Galaxy infrastructure.
• Scalable Processing: Designed to support high-throughput processing of large variant datasets on Galaxy-based compute resources.
• API and Library Integration: Interacts with Galaxy using the Galaxy API or the Bioblend library to manage job execution and data transfer.

Scientific Applications:

• Genomic Variant Analysis: Prepares CLC-derived variant data for snpEff-based functional annotation to support interpretation of genetic variants.
• Metagenomics and Phylogenetics: Integrates annotated variant data into metagenomic analyses and phylogenetic studies that require variant-level annotation.

Methodology:

Converts CLC find_variations output to a snpEff-compatible tabular format and performs the conversion via execution on the Galaxy platform (Galaxy@Pasteur / Institut Pasteur cluster), communicating with Galaxy through the Galaxy API or Bioblend.