Repositories list

• tbvcfreport

  Public
  Generate an interactive HTML-based report from M.tb SnpEff annotated VCF(s)

  neo4jgalaxy-projectvariant-annotations+ 5tuberculosisvcf-filesvcfsnpeffcombat-tb-neodb

  Python

  •

  GNU General Public License v3.0

  •2•2•1•0•Updated Jun 7, 2024Jun 7, 2024

• tb_variant_filter

  Public
  A tool for filtering VCF files (relative to M. tuberculosis H37Rv)

  Python

  •

  GNU General Public License v3.0

  •1•6•4•1•Updated Nov 21, 2023Nov 21, 2023

• deploy_explorer_neodb

  Public
  Python

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated May 20, 2023May 20, 2023

• vcf2neo

  Public
  A tool to import SnpEff annotated files to a Neo4j Graph database

  neo4j-databasegraph-databasevariant-calling+ 3tuberculosispy2neosnpeff

  Python

  •

  GNU General Public License v3.0

  •2•3•0•3•Updated Dec 8, 2022Dec 8, 2022

• tb2neo

  Public
  A tool to aggregate and load TB data to Neo4j

  neo4jgff3genome-annotation+ 2tuberculosispy2neo

  Python

  •

  GNU General Public License v3.0

  •0•1•3•3•Updated Dec 8, 2022Dec 8, 2022

• combat-tb.github.io

  Public
  COMBAT-TB Website

  bioinformaticsneo4j-databasegalaxy-project+ 3workflow-management-systemtuberculosissouth-africa

  CSS

  •2•0•0•0•Updated Aug 31, 2022Aug 31, 2022

• irida-galaxy-deploy

  Public
  🐳 Deploying IRIDA and Galaxy all in one server/VM using Docker or Terraform

  galaxy-projectdockeropenstack+ 2iridairida-galaxy-importer

  HTML

  •

  Apache License 2.0

  •4•3•4•0•Updated Aug 11, 2022Aug 11, 2022

• irida-plugin-builder

  Public
  Build an IRIDA plugin

  Shell

  •

  Apache License 2.0

  •0•1•0•0•Updated May 22, 2022May 22, 2022

• irida-plugin-tb-sample-report

  Public
  M. tuberculosis Variant and Drug Resistance Analysis

  Java

  •

  Apache License 2.0

  •0•0•0•0•Updated Sep 28, 2021Sep 28, 2021

• combattbworkbench-docs

  Public
  Creative Commons Attribution 4.0 International

  •0•0•0•0•Updated Sep 27, 2021Sep 27, 2021

• combat-tb-neodb

  Public
  🐳 combatTB Neo4j Database

  dockerbioinformaticsneo4j+ 5graph-databasetuberculosisapoch37rvcdc1551

  HTML

  •

  GNU General Public License v3.0

  •1•1•0•2•Updated Aug 17, 2021Aug 17, 2021

• irida-plugin-tb-phylogeny

  Public
  IRIDA pipeline to build phylogeny from M. tuberculosis WGS samples

  Java

  •

  Apache License 2.0

  •2•0•0•0•Updated Jul 2, 2021Jul 2, 2021

• combattb_gsea

  Public
  Python

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated May 7, 2021May 7, 2021

• combattbmodel

  Public
  COMBAT-TB model is a Chado inspired graph model for genome annotation.

  neo4jgenome-annotationpy2neo+ 3graph-modelchadocombat-tb-model

  Python

  •

  GNU General Public License v3.0

  •1•2•2•1•Updated Apr 20, 2021Apr 20, 2021

• irida-pipeline-plugins

  Public archive
  Galaxy pipelines as plugin for IRIDA intergration

  analysisphylogeneticsgalaxy-project+ 2iridacombact-tb

  Java

  •1•0•0•0•Updated Feb 3, 2021Feb 3, 2021

• irida

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

  Java

  •

  Apache License 2.0

  •31•0•0•0•Updated Oct 27, 2020Oct 27, 2020

• masters_galaxy_ansible

  Public
  Ansible playbooks for Galaxy servers used during Masters in Bioinformatics

  HCL

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Jul 27, 2020Jul 27, 2020

• neo4j-galaxy-ie

  Public
  🐳 Neo4j Galaxy IE

  galaxy-projectdockerneo4j+ 1quay

  Shell

  •2•0•2•0•Updated Oct 28, 2019Oct 28, 2019

• tb_profiler_galaxy

  Public
  Galaxy wrapper for Jody Phelan's TB-Profiler

  0•0•0•0•Updated Apr 2, 2019Apr 2, 2019

• confil

  Public
  Contamination Filter

  Python

  •

  GNU General Public License v3.0

  •1•0•0•1•Updated Mar 25, 2019Mar 25, 2019

• combat-tb-gx-pipelines

  Public
  Backup of Galaxy Pipelines

  bioinformaticspipelinegalaxy-project+ 1combattb

  Apache License 2.0

  •0•0•0•0•Updated Mar 15, 2019Mar 15, 2019

• TBProfiler

  Public
  Python

  •43•0•0•0•Updated Sep 24, 2018Sep 24, 2018

• vcf_snps_utils

  Public archive
  Custom command line utility tools to manipulate vcf files

  snpsvcfgalaxy-project+ 2vcftoolscombact-tb

  Python

  •

  Apache License 2.0

  •0•0•0•0•Updated Sep 18, 2018Sep 18, 2018

• vcf_from_snvphyl

  Public
  Parses variant report from SNVPhyl and generates annotated (ala. SnpEff) VCF files, using COMBAT-TB eXplorer database for annotation

  Python

  •

  MIT License

  •0•0•0•0•Updated Jun 6, 2018Jun 6, 2018

• refinery-platform

  Public
  The Refinery Platform is a data management, analysis and visualization system for bioinformatics and computational biology applications. The platforms consists of three major components: a data repository with rich metadata capabilities, a workflow engine based on the popular Galaxy system, and visualization tools to support the exploration and …

  JavaScript

  •

  Other

  •24•0•0•0•Updated Jan 9, 2018Jan 9, 2018

• phyloviewer

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Nov 29, 2017Nov 29, 2017

• PHEnix

  Public
  Public Health England SNP calling pipeline.

  Python

  •

  GNU General Public License v3.0

  •8•0•0•0•Updated Nov 14, 2017Nov 14, 2017

• explorer

  Public
  COMBAT-TB Explorer Web Application

  bioinformaticsneo4jtuberculosis

  0•0•2•0•Updated Oct 18, 2017Oct 18, 2017

• combat_tb_utils

  Public
  Utilities modules for COMBAT TB project tools

  Python

  •

  MIT License

  •0•0•0•0•Updated Sep 26, 2017Sep 26, 2017