Technical help sheet

Technical requirements for data analysis

You will require the following tools for executing the practicals in this course:

Assembly and comparative analysis with ViralFlow

Singularity 3.8https://docs.sylabs.io/guides/3.8/user-guide/quick_start.html
ViralFlow with singularity container modehttps://github.com/dezordi/ViralFlow

Phylogenomics methods – discrete phylogeography

beasthttps://anaconda.org/bioconda/beast OR https://github.com/beast-dev/beast-mcmc/releases/
tracerhttps://anaconda.org/bioconda/tracer OR https://github.com/beast-dev/tracer/releases/
figtreehttps://anaconda.org/bioconda/figtree OR https://github.com/rambaut/figtree/releases
SpreaD3https://rega.kuleuven.be/cev/ecv/software/spread3_files/spread3-v0-9-7-1rc.jar

Nextstrain resource

NextstrainInstalling Nextstrain — Nextstrain documentation
Nextstrain datahttps://drive.google.com/drive/folders/1nWIOaJuyEIW8gt-ek8-XopYfBRtYygi8?usp=share_link

Metaviromics

Nextflowhttps://www.nextflow.io/
Dockerhttps://docs.docker.com/engine/install/
VIRifyhttps://github.com/EBI-Metagenomics/emg-viral-pipeline
SPAdeshttps://github.com/ablab/spades
VIRify Databaseshttps://drive.google.com/file/d/1jvGP9dnYx8pkVQciOrFZAJTd3WVRuMCt/view?usp=sharing