VIROSCIENCE

This is the landing page for the EMC Viroscience GitHub.

Direct repository links

EMC-Viroscience.github.io

Repo for the EMC-Viroscience Quarto website

illumina-metagenomic-analysis-manual

This is a manual for viral metagenomic data analysis of Illumina short reads

nanopore-amplicon-analysis-manual

This is a manual for viral amplicon data analysis of Nanopore long reads

bird-surveillance-dashboard

Source code for the bird surveillance dashboard based on the Pathogen Portal data.

SARS-CoV-2_submission

No description available.

Genomic-monitoring-mpox-in-Burundi

Genomic monitoring and tracking of mpox virus Clade Ib after the introduction into Burundi at the end of July until mid-September, 2024

Worp_etal_Global_Sewage_Virome

snakemake workflow and scripts for global urban virome wastewater study (Manuscript in submission Worp et al, 2025)

USUV_submission

Usutu virus submission made easy—this structured template is designed for programmatically submitting raw read samples, runs, and experiment metadata to ENA. Converts tables…

updated_illumina_workflow

A Snakemake workflow for processing Illumina sequencing data, tested and validated on wastewater metagenomics.

Rashidi_et_al-2024-COVID19-brain-apoptosis

Scripts and Data for Rashidi et al 2024 Manuscript

ENA-submission

Script, parser, command used to submit data to ENA

tsv2xmlParser

No description available.