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12 repositories

Grandeur
Public
UPHL's Reference Free Pipeline
docker bioinformatics genomics
docker bioinformatics genomics nextflow ngs phylogenetics illumina denovo-assembly serotyping salmonella
Nextflow
•
GNU General Public License v3.0
•7•29•1•1•Updated Aug 7, 2026Aug 7, 2026
Cecret
Public
Reference-based consensus creation
bioinformatics nextflow phylogenetics
bioinformatics nextflow phylogenetics public-health variant-calling amplicon viral-genomics wastewater mafft ivar
Nextflow
•
MIT License
•31•61•1•0•Updated Aug 7, 2026Aug 7, 2026
General_LW_scripts
Public
The scripts that UPHL uses to download things from basespace and run respective workflows
bioinformatics
bioinformatics
Python
•
GNU General Public License v3.0
•4•2•0•2•Updated Aug 6, 2026Aug 6, 2026
Wastewater-genomic-analysis
Public
Shell
•0•1•1•0•Updated Jul 8, 2026Jul 8, 2026
walkercreek
Public
A Nextflow pipeline for viral genomics (Influenza/RSV) supporting Illumina and Nanopore sequencing of clinical and wastewater samples.
bioinformatics pipeline genomics
bioinformatics pipeline genomics nextflow public-health irma variant-calling influenza illumina oxford-nanopore
Nextflow
•
MIT License
•3•10•0•0•Updated Jun 9, 2026Jun 9, 2026
Donut_Falls
Public
Assembly of Nanopore Sequencing
bioinformatics nanopore nextflow
bioinformatics nanopore nextflow denovo-assembly bandage polishing hybrid-assembly fastp busco unicycler
Nextflow
•
MIT License
•7•17•3•0•Updated May 21, 2026May 21, 2026
Dockerfiles
Public
A collection of Dockerfiles for the images that we use
Dockerfile
•0•0•0•0•Updated Dec 16, 2025Dec 16, 2025
neissflow
Public
Nextflow pipeline for Neisseria gonorrhoeae isolate analysis
Nextflow
•
Apache License 2.0
•2•0•0•0•Updated May 14, 2025May 14, 2025
mycosnp-nf
Public
CDCgov/mycosnp-nf
Nextflow
•
Apache License 2.0
•44•0•0•0•Updated Feb 14, 2025Feb 14, 2025
ICA_Modified_Nextflow_Scripts
Public
To be able to run Nextflow scripts that are published on Github on ICA they must be modified because ICA does not have Nextflow do a gitpull and an ICA user can…
nextflow ica
nextflow ica
Nextflow
•
GNU General Public License v3.0
•0•2•0•0•Updated Sep 6, 2023Sep 6, 2023
Nextstrain_Build
Public
A Nextflow Script that performs a Nextstrain 'Build' which creates a detailed phylogentic visualization that can be seen with the Nextstain Auspice tool.
Nextflow
•
MIT License
•0•0•2•0•Updated Aug 26, 2022Aug 26, 2022
UPHL
Public archive
The fun things we use and share at UPHL
Shell
•
MIT License
•1•5•0•0•Updated Mar 11, 2021Mar 11, 2021

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UPHL-BioNGS

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12 repositories

Grandeur

Cecret

General_LW_scripts

Wastewater-genomic-analysis

walkercreek

Donut_Falls

Dockerfiles

neissflow

mycosnp-nf

ICA_Modified_Nextflow_Scripts

Nextstrain_Build

UPHL

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12 repositories