Oxford MMM

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46 repositories

gnomonicus
Public
Python code to integrate results of tb-pipeline and provide an antibiogram, mutations and variants
antimicrobial-resistance bioinformatics genomics
Python
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Other
•0•4•1•0•Updated Dec 19, 2024Dec 19, 2024
grumpy
Public
Re-implementation of gumpy in rust for speed
Rust
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Other
•0•2•0•0•Updated Dec 19, 2024Dec 19, 2024
piezo
Public
Python
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Other
•0•2•2•0•Updated Dec 5, 2024Dec 5, 2024
FN5
Public
SNP matrix generation with caching to disk to allow fast reloading
C++
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Other
•1•2•0•0•Updated Nov 14, 2024Nov 14, 2024
labbox_backend
Public
The backend files for the LabBox application
Python
•
MIT License
•0•0•0•0•Updated Nov 3, 2024Nov 3, 2024
labbox_frontend
Public
The front-end for the LabBox application
TypeScript
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MIT License
•0•0•0•0•Updated Sep 9, 2024Sep 9, 2024
ukhsa-datafeeds-timeliness-anon
Public
HTML
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MIT License
•0•0•0•0•Updated Aug 21, 2024Aug 21, 2024
tuberculosis_amr_catalogues
Public
Python
•0•5•0•0•Updated Aug 19, 2024Aug 19, 2024
gumpy
Public
Genetics with numpy
bioinformatics
Python
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Other
•1•4•3•0•Updated Jul 24, 2024Jul 24, 2024
flye_medaka_workflow
Public
Nextflow
•1•1•0•1•Updated Apr 19, 2024Apr 19, 2024
collaborative_github_exercise
Public
Copied from https://github.com/RSE-Sheffield/collaborative_github_exercise with thanks!
HTML
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MIT License
•4•0•0•0•Updated Apr 19, 2024Apr 19, 2024
gpas_local_db
Public
Database to hosted locally in the hospital, holding GPAS sourced data plus others
Python
•0•0•0•0•Updated Apr 14, 2024Apr 14, 2024
Illumina_SNIPPY_workflow
Public
Python
•0•0•0•0•Updated Feb 7, 2024Feb 7, 2024
Bugflow_DSL2
Public
Nextflow
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Other
•2•1•0•0•Updated Jan 18, 2024Jan 18, 2024
cdiff_reporting
Public
Python
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Other
•1•0•0•0•Updated Jan 4, 2024Jan 4, 2024
SARS-CoV2_workflows
Public
Nextflow
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MIT License
•3•2•0•0•Updated Nov 19, 2023Nov 19, 2023
ncov2019-artic-nf
Public
A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019
Nextflow
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GNU Affero General Public License v3.0
•88•3•0•0•Updated Nov 19, 2023Nov 19, 2023
testdata-catalog
Public
Reposity to keep the catalog of samples for testing
Shell
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MIT License
•0•1•0•0•Updated Sep 18, 2023Sep 18, 2023
minimal_pathogen_fq_ENA_upload
Public
Python
•0•0•0•0•Updated Jun 12, 2023Jun 12, 2023
catsgo
Public
Command client of SP3 for fetch, run and download.
Python
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MIT License
•2•1•0•0•Updated Mar 22, 2023Mar 22, 2023
runListCompare
Public
Python
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Other
•4•0•0•0•Updated Mar 9, 2023Mar 9, 2023
gpas_adb
Public
GPAS Autonomous Database
Python
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MIT License
•0•0•0•0•Updated Feb 10, 2023Feb 10, 2023
gramnegMMM
Public
Nextflow
•0•0•0•0•Updated Nov 21, 2022Nov 21, 2022
gpas_ena_download
Public
For downloading ENA samples and making them available to the GPAS pipeline
MIT License
•0•0•0•0•Updated Oct 31, 2022Oct 31, 2022
preprocessing
Public
Mycobacterial pre-processing pipeline
Nextflow
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Other
•2•0•1•0•Updated Oct 7, 2022Oct 7, 2022
gpas-tb-CI-testing
Public
Automated end-to-end testing of the GPAS TB pipeline
Shell
•0•0•0•0•Updated Sep 23, 2022Sep 23, 2022
AMR-catalogue-demo
Public
A Jupyter notebook to demonstrate usage of piezo, gumpy and gnomonicus with different AMR catalogues
tuberculosis antimicrobial-resistance
Jupyter Notebook
•0•0•0•0•Updated Sep 20, 2022Sep 20, 2022
TBProfiler-to-GARC
Public
Covert the TBProfiler's TBDB to GARC for use with `piezo`
Python
•0•0•0•0•Updated Sep 16, 2022Sep 16, 2022
catdocs
Public
Documentation for Scalable Pathogen Pipeline Platform (SP3)
Other
•2•0•0•1•Updated Aug 17, 2022Aug 17, 2022
gumpy-tutorial
Public
Simple tutorial using a jupyter notebook to walkthrough how to use gumpy
MIT License
•0•0•0•0•Updated Jun 17, 2022Jun 17, 2022