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Related Experiment Video

Updated: Jan 22, 2026

Generating Whole Bacterial Genomes from Clinical Samples using a Target Enrichment Workflow

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Published on: August 15, 2025

From Permits to Samples: Addressing Key Challenges for High-Quality Reference Genome Generation in Europe.

Katja Reichel¹, Jaakko Pohjoismäki², Jonas J Astrin³

¹Institute of Biology, Dahlem Center of Plant Sciences, Freie Universität Berlin, Berlin, Germany.

Molecular Ecology Resources

|January 21, 2026

Summary

This summary is machine-generated.

Obtaining high-quality reference genomes for biodiversity research is challenging due to complex permit and sample-handling needs. This study provides practical guidance for ethical, legal, and logistical compliance in sample processing for genomic studies.

Keywords:

DNA/RNA preservation European Reference Genome Atlas eukaryotes genome sequencing high molecular weight DNA sampling design

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Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Published on: August 20, 2021

Area of Science:

Genomics
Biodiversity Research
Bioinformatics

Background:

High-quality reference genome assemblies are crucial for understanding biodiversity.
Acquiring these assemblies for many species presents significant logistical and regulatory challenges.
The European Reference Genome Atlas (ERGA) community has encountered and addressed these issues.

Purpose of the Study:

To provide practical guidance on permit and sample-handling procedures for obtaining high-quality genomic data.
To address challenges in ethical and legal compliance, species identification, sample integrity, and DNA isolation.
To support both small-scale and large-scale genomic initiatives.

Main Methods:

Reviewing and synthesizing experiences from the ERGA community regarding pre-sequencing procedures.
Focusing on permit acquisition, ethical/legal compliance, species verification, sample transport, and nucleic acid isolation.
Compiling practical guidance and examples from diverse regions and taxa.

Main Results:

Identified key challenges in permit and sample handling for genome sequencing.
Highlighted the importance of taxonomic expertise, vouchering, biobanking, and cold-chain management.
Emphasized adherence to packaging, shipping regulations, and the need for harmonized metadata reporting.

Conclusions:

Effective sample processing, including ethical sourcing and preservation, is critical for successful genome assembly.
Context-specific strategies and harmonized international protocols are essential for advancing biodiversity genomics.
The recommendations aim to streamline sample collection and processing for future genomic studies.