Public Health Bioinformatics

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44 repositories

irida-plugin-tbprofiler
Public
tuberculosis antimicrobial-resistance irida-pipeline
tuberculosis antimicrobial-resistance irida-pipeline
Java
•
Apache License 2.0
•1•1•1•1•Updated Mar 27, 2026Mar 27, 2026
irida-plugin-snippy-single
Public
Call SNPs and indels between a reference genome and your sequence data
Java
•0•0•2•1•Updated Mar 27, 2026Mar 27, 2026
irida-plugin-micall-lite
Public
Human RNA virus genotyping
bioinformatics-pipeline galaxy viral-genomics
bioinformatics-pipeline galaxy viral-genomics irida-pipeline
Java
•
Apache License 2.0
•0•0•1•1•Updated Mar 27, 2026Mar 27, 2026
irida-plugin-species-abundance
Public
Estimate the relative abundance of sequence reads originating from different species in a sample using the IRIDA system
metagenomics bioinformatics-pipeline microbial-genomics
metagenomics bioinformatics-pipeline microbial-genomics species-abundance-distributions species-identification irida-pipeline
Java
•
Apache License 2.0
•3•0•1•2•Updated Mar 27, 2026Mar 27, 2026
irida-plugin-snippy-phylogenomics
Public
Call core SNPs agains a reference genome for a set of bacterial isolates, and build a phylogenetic tree based on the core-genome SNP information.
bioinformatics-pipeline microbial-genomics phylogenomics-pipeline
bioinformatics-pipeline microbial-genomics phylogenomics-pipeline irida-pipeline
Java
•1•2•3•2•Updated Mar 27, 2026Mar 27, 2026
irida-plugin-mlst
Public
Determine the MLST sequence type for samples using PubMLST schemes in the IRIDA system
bioinformatics-pipeline microbial-genomics mlst
bioinformatics-pipeline microbial-genomics mlst galaxy irida-pipeline microbial-subtyping
Java
•2•0•3•1•Updated Mar 27, 2026Mar 27, 2026
galaxy_tools
Public
tools genomics microbial-genomics
tools genomics microbial-genomics usegalaxy genomic-workflows
Python
•1•0•0•0•Updated Jan 30, 2025Jan 30, 2025
pubmlst_client
Public
List and download schemes from pubMLST.org and other BIGSDB servers
bioinformatics mlst rest-client
bioinformatics mlst rest-client
Python
•
MIT License
•5•10•0•1•Updated Oct 14, 2024Oct 14, 2024
irida-plugin-tbprofiler-multisample
Public
Java
•
Apache License 2.0
•0•0•0•0•Updated Jul 13, 2023Jul 13, 2023
compute_canada_cloud
Public
0•0•0•0•Updated Apr 29, 2021Apr 29, 2021
snakemake_demo
Public
Jupyter Notebook
•
MIT License
•1•0•0•0•Updated Feb 25, 2021Feb 25, 2021
decision-tree
Public
A question and answer web form system for exploring the research questions and datasets pertinent to an emerging infectious disease outbreak.
Makefile
•1•1•0•0•Updated Jan 15, 2021Jan 15, 2021
COVID19-QC
Public
Python
•
MIT License
•0•0•0•0•Updated Nov 10, 2020Nov 10, 2020
irida-plugin-plasmid-screen
Public
bioinformatics-pipeline galaxy antimicrobial-resistance
bioinformatics-pipeline galaxy antimicrobial-resistance irida-pipeline plasmid-genomics
Java
•0•0•1•1•Updated Oct 13, 2020Oct 13, 2020
irida-plugin-tetyper
Public
Determine the sequence type of specific transposable elements in bacterial isolates.
bioinformatics-pipeline microbial-genomics galaxy
bioinformatics-pipeline microbial-genomics galaxy transposable-elements irida-pipeline
Java
•
Apache License 2.0
•0•0•1•1•Updated Oct 13, 2020Oct 13, 2020
irida-plugin-resistance-screen
Public
Detect the presence of specific resistance genes in a sample using the IRIDA system
bioinformatics-pipeline microbial-genomics antimicrobial-resistance
bioinformatics-pipeline microbial-genomics antimicrobial-resistance irida-pipelines
Java
•
Apache License 2.0
•2•0•1•1•Updated Oct 13, 2020Oct 13, 2020
lexmapr_ontology
Public
An ontology that contains various agency category schemes that Lexmapr can use to report matched terms by.
Creative Commons Zero v1.0 Universal
•1•0•0•1•Updated Aug 10, 2020Aug 10, 2020
ontofetch
Public
Ontofetch is a command line tool to fetch branches of terms from a given local file or internet based ontology URL. This is output in JSON format, and includes …
Python
•3•3•1•0•Updated Jun 24, 2020Jun 24, 2020
blast_reporting
Public
A Galaxy tool that converts an NCBI BLAST XML format search result into 12, 24, 26 or custom column tabular and HTML reports.
Python
•
Other
•2•1•2•1•Updated Feb 27, 2020Feb 27, 2020
purl.obolibrary.org
Public
A new system for managing OBO PURLs
Python
•
BSD 3-Clause "New" or "Revised" License
•136•0•0•0•Updated Dec 20, 2019Dec 20, 2019
tutorial
Public
Protege tutorial resources
Other
•0•1•0•0•Updated Nov 15, 2019Nov 15, 2019
flu_classification_suite
Public
:syringe: :bar_chart: Flu Classification Suite
Python
•1•5•2•0•Updated Nov 12, 2019Nov 12, 2019
cpo-pipeline
Public
An analysis pipeline for the purpose of investigating Carbapenemase-Producing Organisms.
Python
•
MIT License
•2•1•8•0•Updated Jun 14, 2019Jun 14, 2019
sequdas-qc
Public
Python
•
MIT License
•2•0•1•1•Updated Apr 30, 2019Apr 30, 2019
software-development-best-practices
Public
0•0•0•0•Updated Apr 2, 2019Apr 2, 2019
irida
Public
Canada’s Integrated Rapid Infectious Disease Analysis Platform for Genomic Epidemiology
Java
•
Apache License 2.0
•34•0•0•0•Updated Mar 20, 2019Mar 20, 2019
sequdas-web
Public
Python
•
MIT License
•0•0•3•1•Updated Mar 20, 2019Mar 20, 2019
clade_assignment
Public
Python scripts to assign clade designations to influenza amino acid fasta files.
Python
•2•0•0•0•Updated Jan 8, 2019Jan 8, 2019
routine-nanopore-processing
Public
Shell
•
GNU General Public License v3.0
•1•0•1•0•Updated Jan 3, 2019Jan 3, 2019
sequdas-uploader
Public
Python
•
MIT License
•0•0•0•0•Updated Dec 4, 2018Dec 4, 2018

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