UPHL-BioNGS

All

11 repositories

Grandeur
Public
UPHL's Reference Free Pipeline
docker nextflow singularity illumina serotyping prokaryotes bioinformatics genomics ngs
Nextflow
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GNU General Public License v3.0
•7•25•8•1•Updated Jan 18, 2025Jan 18, 2025
Donut_Falls
Public
Basic workflow for nanopore sequencing data
nanopore nextflow denovo-assembly polishing bioinformatics
Nextflow
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MIT License
•7•15•7•1•Updated Jan 16, 2025Jan 16, 2025
Cecret
Public
Reference-based consensus creation
nextflow amplicon sars-cov-2 monkeypox bioinformatics
Nextflow
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MIT License
•27•51•8•0•Updated Jan 14, 2025Jan 14, 2025
walkercreek
Public
A nextflow pipeline for influenza genome analysis
Nextflow
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MIT License
•1•6•1•1•Updated Jan 9, 2025Jan 9, 2025
General_LW_scripts
Public
The scripts that UPHL uses to download things from basespace and run respective workflows
bioinformatics
Python
•
GNU General Public License v3.0
•2•2•0•7•Updated Jan 7, 2025Jan 7, 2025
Dockerfiles
Public
A collection of Dockerfiles for the images that we use
Dockerfile
•0•0•0•0•Updated Nov 4, 2024Nov 4, 2024
mycosnp-nf
Public
CDCgov/mycosnp-nf
Nextflow
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Apache License 2.0
•35•0•0•0•Updated Sep 12, 2024Sep 12, 2024
Wastewater-genomic-analysis
Public
Python
•0•1•1•0•Updated Aug 12, 2024Aug 12, 2024
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 cannot pass config or param files.
nextflow ica
Nextflow
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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
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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
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MIT License
•1•5•0•0•Updated Mar 11, 2021Mar 11, 2021