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/
Biodiversity Genomics Europe, funded by Horizon Europe call HORIZON-CL6-2021-BIODIV-01-01, aims at aligning the resources and research agendas of both DNA barcoding and reference genome generation, thus opening the door for a true quantum leap in biodiversity genomics research in Europe.
Despite ground-breaking developments in both DNA barcoding and full genome sequencing, there remains a critical need to develop and strengthen functioning communities of practice ...
Teams: Vertebrate Genomes Pipelines in Galaxy, Biodiversity Genomics Europe (general)
Web page: https://biodiversitygenomics.eu/
This is a general team for the BGE project for any members affiliated directly or indirectly with the BGE project.
To request joining this team, make sure sure your WorkflowHub institution matches one of the listed BGE partners.
Space: Biodiversity Genomics Europe (BGE)
Public web page: https://biodiversitygenomics.eu/
Start date: 1st Sep 2022
End date: 28th Feb 2026
Space: iBOL Europe
Public web page: Not specified
Space: iBOL Europe
Public web page: Not specified
Space: iBOL Europe
Public web page: Not specified
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 ...
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.
