Public-Health-Bioinformatics/cpo-pipeline

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Language
Python
License
MIT License
Created about 6 years ago
Updated over 5 years ago

Public-Health-Bioinformatics/cpo-pipeline

Public-Health-Bioinformatics

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

pubmlst_client

List and download schemes from pubMLST.org and other BIGSDB servers

kipper

command line versioning tool for large key-value text files

galaxy-tool-tutorials

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

flu_classification_suite

💉 📊 Flu Classification Suite

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.

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

tutorial

Protege tutorial resources

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.

decision-tree

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

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.

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.