Repositories
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decision-tree
A question and answer web form system for exploring the research questions and datasets pertinent to an emerging infectious disease outbreak.
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irida-plugin-snippy-single
Call SNPs and indels between a reference genome and your sequence data
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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.
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irida-plugin-tetyper
Determine the sequence type of specific transposable elements in bacterial isolates.
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irida-plugin-species-abundance
Estimate the relative abundance of sequence reads originating from different species in a sample using the IRIDA system
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irida-plugin-resistance-screen
Detect the presence of specific resistance genes in a sample using the IRIDA system
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pubmlst_client
List and download schemes from pubMLST.org and other BIGSDB servers
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LexMapr
LexMapr: A Lexicon and Rule-Based Tool for Translating Short Biomedical Specimen Descriptions into Semantic Web Ontology Terms
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lexmapr_ontology
An ontology that contains various agency category schemes that Lexmapr can use to report matched terms by.
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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.
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irida-plugin-micall-lite
Human RNA virus genotyping
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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.
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tutorial
Protege tutorial resources
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flu_classification_suite
💉 📊 Flu Classification Suite -
irida-plugin-mlst
Determine the MLST sequence type for samples using PubMLST schemes in the IRIDA system
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cpo-pipeline
An analysis pipeline for the purpose of investigating Carbapenemase-Producing Organisms.
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irida
Forked from phac-nml/iridaCanada’s Integrated Rapid Infectious Disease Analysis Platform for Genomic Epidemiology
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clade_assignment
Python scripts to assign clade designations to influenza amino acid fasta files.