CDPHE GSP Bioinformatics Unit

All

14 repositories

CDPHE-H5-influenza
Public
Workflows and scripts for the assembly and analysis of H5 influenza
bioinformatics pipeline wdl influenza
Jupyter Notebook
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GNU General Public License v3.0
•0•0•4•1•Updated Dec 3, 2025Dec 3, 2025
CDPHE-docker-builds
Public
Docker builds for CDPHE pipelines and workflows.
docker bioinformatics tools
Python
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GNU General Public License v3.0
•0•0•2•0•Updated Dec 3, 2025Dec 3, 2025
CDPHE-Viral-Amplicon-WDL
Public
0•0•0•1•Updated Dec 3, 2025Dec 3, 2025
cdphe-influenza-wastewater-analysis
Public
WDL workflows for 1) Freyja analysis and 2) alignment of clinical samples amplified with universal primers to Freyja references
WDL
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GNU General Public License v3.0
•0•0•0•0•Updated Nov 21, 2025Nov 21, 2025
CDPHE-SARS-CoV-2
Public
Workflows and scripts for the assembly and analysis of SARS-CoV-2 whole genome tiled amplicon sequencing.
bioinformatics pipeline wdl sars-cov-2
Python
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GNU General Public License v3.0
•1•5•12•0•Updated Nov 21, 2025Nov 21, 2025
CDPHE-RSV
Public
Workflows and scripts for the assembly and analysis of RSV whole genome tiled amplicon sequencing.
bioinformatics pipeline wdl rsv
WDL
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GNU General Public License v3.0
•0•1•4•1•Updated Nov 11, 2025Nov 11, 2025
CDPHE-analysis-tools
Public
Useful workflows and tasks for CDPHE pipelines.
bioinformatics tools wdl
WDL
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Other
•0•1•0•0•Updated Oct 31, 2025Oct 31, 2025
wdl-shared
Public
WDL
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GNU General Public License v3.0
•0•0•1•0•Updated Oct 14, 2025Oct 14, 2025
ncbi-cluster-tracker
Public
Create standalone HTML reports for tracking SNP clusters within NCBI Pathogen Detection
bioinformatics pathogen-genomics
Python
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GNU General Public License v3.0
•0•2•4•0•Updated Aug 21, 2025Aug 21, 2025
CDPHE-Seasonal-Influenza-Tiled-Amplicon-Sequencing
Public
Targeted tiled amplicon based protocol for sequencing the Hemagglutinin (HA) gene segment of seasonal Influenza A and Influenza B virus from wastewater at high depth of coverage
GNU General Public License v3.0
•0•1•0•0•Updated Aug 10, 2025Aug 10, 2025
CDPHE-Enterovirus
Public
Workflows and scripts for the assembly and analysis of enterovirus whole genome sequencing.
bioinformatics pipeline wdl enterovirus
WDL
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GNU General Public License v3.0
•0•0•0•0•Updated Jul 28, 2025Jul 28, 2025
.github
Public
Repository for our GitHub Organization.
0•0•0•0•Updated Jul 18, 2025Jul 18, 2025
CDPHE-influenza
Public
Workflows and scripts for the assembly and analysis of influenza whole genome amplicon sequencing.
bioinformatics pipeline wdl influenza
WDL
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GNU General Public License v3.0
•1•2•2•0•Updated Jul 14, 2025Jul 14, 2025
CDPHE-publications
Public
Repository of code used in CDPHE publications.
bioinformatics publications
Python
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GNU General Public License v3.0
•0•0•0•0•Updated Jun 9, 2023Jun 9, 2023