Pinned Repositories
blast_comparison
This is a Galaxy tool to compare 24 column tabular blast search results to see differences. Used where same search is conducted against two versions of a database to determine how the database has changed and whether there are any issues with the database.
cpo-pipeline
An analysis pipeline for the purpose of investigating Carbapenemase-Producing Organisms.
flu_classification_suite
:syringe: :bar_chart: Flu Classification Suite
galaxy-tool-tutorials
Galaxy tool training materials being developed for in-house workshops.
irida-plugin-snippy-phylogenomics
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.
irida-plugin-tbprofiler
kipper
command line versioning tool for large key-value text files
metadata_manager
This is a spreadsheet application to facilitate tracking, reporting, exchange, and submission of metadata for various projects involving enteric bacteria surveillance. This user-friendly entry form contains fields pertaining to isolate collection and sequencing, isolate typing, geographical information, sample source, clinical details and environmental descriptors.
ontofetch
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 term label, definition, broad, narrow, exact and unspecified) synonyms.
pubmlst_client
List and download schemes from pubMLST.org and other BIGSDB servers
Public Health Bioinformatics's Repositories
Public-Health-Bioinformatics/pubmlst_client
List and download schemes from pubMLST.org and other BIGSDB servers
Public-Health-Bioinformatics/flu_classification_suite
:syringe: :bar_chart: Flu Classification Suite
Public-Health-Bioinformatics/ontofetch
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 term label, definition, broad, narrow, exact and unspecified) synonyms.
Public-Health-Bioinformatics/irida-plugin-snippy-phylogenomics
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.
Public-Health-Bioinformatics/blast_reporting
A Galaxy tool that converts an NCBI BLAST XML format search result into 12, 24, 26 or custom column tabular and HTML reports.
Public-Health-Bioinformatics/cpo-pipeline
An analysis pipeline for the purpose of investigating Carbapenemase-Producing Organisms.
Public-Health-Bioinformatics/decision-tree
A question and answer web form system for exploring the research questions and datasets pertinent to an emerging infectious disease outbreak.
Public-Health-Bioinformatics/irida-plugin-tbprofiler
Public-Health-Bioinformatics/tutorial
Protege tutorial resources
Public-Health-Bioinformatics/clade_assignment
Python scripts to assign clade designations to influenza amino acid fasta files.
Public-Health-Bioinformatics/compute_canada_cloud
Public-Health-Bioinformatics/COVID19-QC
Public-Health-Bioinformatics/galaxy_tools
Public-Health-Bioinformatics/irida
Canada’s Integrated Rapid Infectious Disease Analysis Platform for Genomic Epidemiology
Public-Health-Bioinformatics/irida-plugin-micall-lite
Human RNA virus genotyping
Public-Health-Bioinformatics/irida-plugin-mlst
Determine the MLST sequence type for samples using PubMLST schemes in the IRIDA system
Public-Health-Bioinformatics/irida-plugin-plasmid-screen
Public-Health-Bioinformatics/irida-plugin-resistance-screen
Detect the presence of specific resistance genes in a sample using the IRIDA system
Public-Health-Bioinformatics/irida-plugin-snippy-single
Call SNPs and indels between a reference genome and your sequence data
Public-Health-Bioinformatics/irida-plugin-species-abundance
Estimate the relative abundance of sequence reads originating from different species in a sample using the IRIDA system
Public-Health-Bioinformatics/irida-plugin-tbprofiler-multisample
Public-Health-Bioinformatics/irida-plugin-tetyper
Determine the sequence type of specific transposable elements in bacterial isolates.
Public-Health-Bioinformatics/lexmapr_ontology
An ontology that contains various agency category schemes that Lexmapr can use to report matched terms by.
Public-Health-Bioinformatics/purl.obolibrary.org
A new system for managing OBO PURLs
Public-Health-Bioinformatics/routine-nanopore-processing
Public-Health-Bioinformatics/sequdas-qc
Public-Health-Bioinformatics/sequdas-uploader
Public-Health-Bioinformatics/sequdas-web
Public-Health-Bioinformatics/snakemake_demo
Public-Health-Bioinformatics/software-development-best-practices