DNA extraction and COX1 PCR for subsequent sequencing on PacBio Sequel

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

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.

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.

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. ...

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 ...

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 ...

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.

Contents

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

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 ...