InformaticsGuide.md

Bacterial Genomic Surveillance - Ireland and Northern Ireland Informatics Guide

Software used during the course

Software	Version (if not latest)	Module	Environment
Samtools	1.19.2	Mapping + Phylogeny / Genome Annotation	Conda base
BWA	0.7.17	Mapping + Phylogeny	Conda base
Snippy	4.0.2 / 0.11.0	Mapping + Phylogeny / Genome Annotation	conda activate snippy-env
IQ-TREE 2	2.4.0	Mapping + Phylogeny	Conda base
Gubbins	3.3+	Mapping + Phylogeny	conda activate gubbins-env
FastBAPS	Command-line version	Mapping + Phylogeny	Conda base
FigTree	1.4.4	Mapping + Phylogeny	Conda base
ETE Toolkit	3.1.3	Mapping + Phylogeny	Conda base
Unicycler	0.5.1	Assembly Comparison	Conda base
Dragonflye	1.2.1	Assembly Comparison	conda activate dragonflye-env
QUAST	5.3.0	Assembly Comparison	conda activate quast-env
NUCmer	3.23	Assembly Comparison	Conda base
Google Chrome	Latest	Web Tools for GenEpi	System installation
Firefox	Latest	Web Tools for GenEpi	System installation
Artemis	18.2.0	Genome Annotation	Conda base
ACT	18.1.x	Genome Annotation	Conda base
FastQC	0.12.1	Genome Annotation	Conda base
Trim Galore	0.6.10	Genome Annotation	conda activate ariba-env
ARIBA	2.14.6	Genome Annotation	conda activate ariba-env
SPAdes	3.15.5	Genome Annotation	Conda base
ABACAS	1.3.1	Genome Annotation	Conda base
BLAST+	Latest installed	Genome Annotation	Conda base
Bakta	Latest installed	Genome Annotation	Conda base
RATT	Latest installed	Comparative Genomics	Conda base
Filtlong	0.2.1	Sequencing & QC	Conda base
NanoPlot	1.44.1	Sequencing & QC	Conda base
Roary	Latest installed	Pan-genome Analysis	conda activate roary-env
Panaroo	1.1.2	Pan-genome Analysis	conda activate panaroo-env
Docker	28.2.2	Containerisation	System installation
Kraken2	Latest installed	Taxonomic Classification	conda activate kraken2-env
Kraken2 Standard-8 Database	20260226 release	Taxonomic Classification	/home/vboxuser/databases/kraken2/standard8

Conda Environments

Conda environments allow software and dependencies to be installed in isolated environments. This avoids version conflicts between tools and makes software easier to manage.

View all available environments

conda env list

or

conda info --envs

Example output:

# conda environments:
#
base                  *  /home/vboxuser/miniconda3
snippy-env               /home/vboxuser/miniconda3/envs/snippy-env
gubbins-env              /home/vboxuser/miniconda3/envs/gubbins-env
kraken2-env              /home/vboxuser/miniconda3/envs/kraken2-env

The * indicates the currently active environment.

Activate an environment

Replace <env-name> with the desired environment name:

conda activate <env-name>

Examples:

conda activate snippy-env
conda activate gubbins-env
conda activate kraken2-env

Return to the base environment

conda activate base

Deactivate the current environment

conda deactivate

This returns you to the previous environment, typically base.

Check which environment is currently active

echo $CONDA_DEFAULT_ENV

or

conda info --envs

Check software installed in the current environment

conda list

Check whether a tool is available in the current environment

which samtools
which snippy
which kraken2

Informatics Set-Up

For installation and setup, please refer to the following guide:

• Oracle VM VirtualBox Installation Guide – Detailed instructions for installing and configuring VirtualBox on different operating systems. (Note: Separate installations are needed for Intel-based and ARM-based Macs, and the VDI files will differ.)

The Host Operating System Requirements are:

• RAM requirement: 8GB (preferably 12GB)
  
• Processor requirement: 4 processors (preferably 8)
  
• Hard disk space: 200GB
  
• Admin rights to the computer
  

Citing and Re-using Course Material

The course data are free to reuse and adapt with appropriate attribution. All course data in these repositories are licensed under the Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0).

Each course landing page is assigned a DOI via Zenodo, providing a stable and citable reference. These DOIs can be found on the respective course landing pages and can be included in CVs or research publications, offering a professional record of the course contributions.

Interested in attending a course?

Take a look at what courses are coming up at Wellcome Connecting Science Courses & Conference Website.

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