Barcode Gene Extractor & Evaluator (BGEE) Snakemake workflow

Snakemake workflow for recovering high-quality barcode sequences from genome skim data, built around MitoGeneExtractor and adapted for genome skims of museum specimens.

Contents

• Requirements
• Workflow
• Running
• Cluster configuration
• Results structure
• Integrated and supplementary scripts ...

Barcode Gene Extractor & Evaluator (BGEE) Snakemake workflow

Snakemake workflow for recovering high-quality barcode sequences from genome skim data, built around MitoGeneExtractor and adapted for genome skims of museum specimens.

Contents

• Requirements
• Workflow
• Running
• Cluster configuration
• Results structure
• Integrated and supplementary scripts ...

Gene_fetch

This tool fetches gene sequences from NCBI databases based on taxonomy IDs (taxids) or taxonomic information. It can retrieve both protein and nucleotide sequences for various genes, including protein-coding genes (e.g., cox1, cytb, rbcl, matk) and rRNA genes (e.g., 16S, 18S).

Feature highlight

• Fetch protein and/or nucleotide sequences from NCBI GenBank database.
• Handles both direct nucleotide sequences and protein-linked nucleotide searches (CDS extraction includes fallback ...

Gene_fetch

This tool fetches gene sequences from NCBI databases based on taxonomy IDs (taxids) or taxonomic information. It can retrieve both protein and nucleotide sequences for various genes, including protein-coding genes (e.g., cox1, cytb, rbcl, matk) and rRNA genes (e.g., 16S, 18S).

Feature highlight

• Fetch protein and/or nucleotide sequences from NCBI GenBank database.
• Handles both direct nucleotide sequences and protein-linked nucleotide searches (CDS extraction includes fallback ...