public-health-bioinformatics Goto Github PK

aggregate_linelisting

Transforms fasta files of flu antigenic site amino acids into aggregated line lists, comparing antigenic maps to that of a reference sequence and collapsing and enumerating identical sequences.

antigenic_site_extraction

Extracts antigenic amino acids from flu sequence, using a specific index array (i.e. for H3, H1 etc.).

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.

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.

change_fasta_deflines

Renames definition lines in fasta files.

clade_assignment

Python scripts to assign clade designations to influenza amino acid fasta files.

compute_canada_cloud

covid19-qc

cpo-pipeline

An analysis pipeline for the purpose of investigating Carbapenemase-Producing Organisms.

decision-tree

A question and answer web form system for exploring the research questions and datasets pertinent to an emerging infectious disease outbreak.

flu_classification_suite

:syringe: :bar_chart: Flu Classification Suite

galaxy-tool-tutorials

Galaxy tool training materials being developed for in-house workshops.

galaxy_tools

irida

Canada’s Integrated Rapid Infectious Disease Analysis Platform for Genomic Epidemiology

irida-plugin-micall-lite

Human RNA virus genotyping

irida-plugin-mlst

Determine the MLST sequence type for samples using PubMLST schemes in the IRIDA system

irida-plugin-plasmid-screen

irida-plugin-resistance-screen

Detect the presence of specific resistance genes in a sample using the IRIDA system

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-snippy-single

Call SNPs and indels between a reference genome and your sequence data

irida-plugin-species-abundance

Estimate the relative abundance of sequence reads originating from different species in a sample using the IRIDA system

irida-plugin-tbprofiler

irida-plugin-tbprofiler-multisample

irida-plugin-tetyper

Determine the sequence type of specific transposable elements in bacterial isolates.

kipper

command line versioning tool for large key-value text files

lexmapr_ontology

An ontology that contains various agency category schemes that Lexmapr can use to report matched terms by.

linelisting

Transforms fasta files of flu antigenic site amino acids into line lists, comparing antigenic maps to that of a reference sequence.

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.

minion-data-transfer

Script to handle uploading minion fast5 files to a server for further processing

obofoundry.github.io

OBO Foundry Ontology Registry