iBOL Europe
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
For metabarcoding head to our Metabarcoding Team
If you would like to join iBOL Europe you can become member here: https://iboleurope.org/
Web page: https://iboleurope.org/
Funding details: Related items
https://orcid.org/0000-0002-0979-5896
Bioinformatician on Biodiversity Genomics Europe
Space: iBOL Europe
Public web page: Not specified
Space: iBOL Europe
Public web page: Not specified
Space: iBOL Europe
Public web page: Not specified
Space: iBOL Europe
Public web page: Not specified
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Creators: Ben Price, Owain Powell, Alyssa Paul, Carla Gustave, Jordan Beasley
Submitter: Ben Price
DNA extraction and COX1 PCR for subsequent sequencing on PacBio Sequel
Creators: Alessio Iannucci, Samantha Rossini
Submitter: Ben Price
This workflow uses a slightly modified version of the Santa Cruz Reaction (SCR) protocol by Kapp et al. 2021 for library building of museum specimens. The reaction volumes can be halved to reduce reagent costs, lower volumes have not been tested yet. Please cite the original publication if using this method: https://doi.org/10.1093/jhered/esab012
Creators: Alyssa Paul, Carla Gustave, Owain Powell, Ben Price
Submitter: Ben Price
SOP for DNA extraction and Illumina amplicon library preparation of soil core samples collected for the Case Study "Characterization of Prokaryotic and Eukaryotic Biodiversity from Soil Samples" withing the scope of BGE (Biodiversity Genomics Europe) project.
Creators: Cátia Chaves, Laura Najera Cortazar, Filipa Martins, Sten Anslan, Albano Beja-Pereira, Maria Magalhães, Ben Price
Submitter: Cátia Chaves
SOP for DNA extraction and Illumina amplicon library preparation of encapsulated water samples collected for the Case Study "Detection of Non-Indigenous Marine Species from Port Water Samples" withing the scope of BGE (Biodiversity Genomics Europe) project.
Creators: Cátia Chaves, Laura Najera Cortazar, Filipa Martins, Joana Veríssimo, Glen Dunshea, Ben Price
Submitter: Cátia Chaves
Within the Biodiversity Genomics Europe project, the "High Mountain Systems - Arthropods" case study was designed to evaluate how arthropod communities change along altitudinal gradients in seven selected mountain systems across different countries in Europe, establishing baseline sampling in mountain ranges to track biodiversity shifts associated with climate change. This SOP describes the sampling design and fieldwork methodology for retrieving arthropod bulk samples for metabarcoding analyses. ...
Creators: Laura Najera Cortazar, Sonia Ferreira, Vanessa Mata, Pedro Beja
Submitter: Laura Najera Cortazar
Within the Biodiversity Genomics Europe project, the "Ecological Restoration - Soil" case study was designed to evaluate changes in soil biodiversity during the process of ecological succession, sampling a chronosequence of replicated plots at different stages of restoration since land abandonment. The present SOP describes soil sampling under sterile and cold conditions for metabarcoding analyses. This case study involved sampling four successional stages, represented by specific vegetation types ...
Creators: Laura Najera Cortazar, Albano Beja-Pereira , Pedro Beja
Submitter: Laura Najera Cortazar
Within the Biodiversity Genomics Europe project, the "Pollinator Communities" case study was designed to evaluate pollinator diversity in urban gardens in comparison with agricultural fields, to understand the role of urban habitats for pollinator conservation. This SOP describes the sampling design and Malaise trap fieldwork to retrieve pollinator bulk samples for metabarcoding analysis. This case study involved paired sampling, choosing one large garden and one agricultural field with no more ...
Creators: Laura Najera Cortazar, Sonia Ferreira, Pedro Beja
Submitter: Laura Najera Cortazar
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
NGS Equimolar Pooling Calculator
A web-based tool for calculating equimolar pooling volumes from complex sub-pools for Next-Generation Sequencing (NGS).
About
This calculator helps researchers determine the correct volumes to take from each pool when combining multiple complex sub-pools of NGS libraries for sequencing. It ensures that each individual sample contributes an equal number of molecules to the final sequencing run, resulting in more balanced coverage.
Features
- Calculate ...
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 ...
