Dan Parsons
Bioinformatician on Biodiversity Genomics Europe
SEEK ID: https://workflowhub.eu/people/1022
Location:
United Kingdom
ORCID:
https://orcid.org/0000-0002-5246-0725
Joined: 15th Apr 2025
Expertise: Bioinformatics, Molecular Biology
Tools: Not specified
Their tagsRelated items
Welcome to the iBOL Europe Space!
Here we collect, curate and develop SOPs and pipelines to extract, sequence, assemble and publish DNA barcodes, genome skims and DNA metabarcodes for all eukaryotic life.
For fresh sample barcoding head to our Barcoding Team
For museum specimen genome skimming head to our Museum Skimming Team
For barcode data wrangling head to our Barcode Data Team ...
Teams: iBOL Europe Museum Skimming, iBOL Europe Metabarcoding, iBOL Europe Barcoding, iBOL Europe Barcode Data
Web page: https://iboleurope.org/
Space: iBOL Europe
Public web page: Not specified
Space: iBOL Europe
Public web page: Not specified
Space: iBOL Europe
Public web page: Not specified
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
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
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 ...
