EMC-Viroscience

All

12 repositories

nanopore-amplicon-analysis-manual
Public
This is a manual for viral amplicon data analysis of Nanopore long reads
oxford-nanopore viral-genomics amplicon-sequencing snakemake-workflow consensus-sequence
Python
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GNU General Public License v3.0
•1•0•0•0•Updated Dec 4, 2025Dec 4, 2025
illumina-metagenomic-analysis-manual
Public
This is a manual for viral metagenomic data analysis of Illumina short reads
metagenomics illumina viral-metagenomics snakemake-workflow short-reads
Python
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GNU General Public License v3.0
•1•0•0•0•Updated Nov 26, 2025Nov 26, 2025
EMC-Viroscience.github.io
Public
Repo for the EMC-Viroscience Quarto website
bioinformatics quarto viroscience
Python
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Other
•1•0•0•0•Updated Nov 26, 2025Nov 26, 2025
bird-surveillance-dashboard
Public
Source code for the bird surveillance dashboard based on the Pathogen Portal data.
dashboards arboviruses quarto
MIT License
•1•0•0•0•Updated Nov 20, 2025Nov 20, 2025
SARS-CoV-2_submission
Public
Python
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MIT License
•1•0•0•0•Updated Jul 18, 2025Jul 18, 2025
Genomic-monitoring-mpox-in-Burundi
Public
Genomic monitoring and tracking of mpox virus Clade Ib after the introduction into Burundi at the end of July until mid-September, 2024
1•0•0•0•Updated Apr 7, 2025Apr 7, 2025
Worp_etal_Global_Sewage_Virome
Public
snakemake workflow and scripts for global urban virome wastewater study (Manuscript in submission Worp et al, 2025)
Python
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Apache License 2.0
•1•0•0•0•Updated Mar 19, 2025Mar 19, 2025
USUV_submission
Public
Usutu virus submission made easy—this structured template is designed for programmatically submitting raw read samples, runs, and experiment metadata to ENA. Converts tables to XML, supports adding or modifying metadata, retrieves submission receipts, and includes metadata accessions.
Python
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MIT License
•1•0•0•0•Updated Feb 12, 2025Feb 12, 2025
updated_illumina_workflow
Public
A Snakemake workflow for processing Illumina sequencing data, tested and validated on wastewater metagenomics.
Python
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Apache License 2.0
•1•0•0•0•Updated Feb 6, 2025Feb 6, 2025
Rashidi_et_al-2024-COVID19-brain-apoptosis
Public
Scripts and Data for Rashidi et al 2024 Manuscript
ImageJ Macro
•1•0•0•0•Updated Mar 5, 2024Mar 5, 2024
ENA-submission
Public
Script, parser, command used to submit data to ENA
Perl
•0•0•0•0•Updated Oct 24, 2022Oct 24, 2022
tsv2xmlParser
Public
Python
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MIT License
•1•0•0•0•Updated May 5, 2021May 5, 2021