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    34 repositories

    • chewBBACA

      Public
      BSR-Based Allele Calling Algorithm
      bioinformaticsgenomicsmlstbacteriacgmlstoutbreak-detectionwgmlstbacterial-genome-analysisallele-callingbacterial-typing
      HTML
      •
      GNU General Public License v3.0
      •33•146•22•2•Updated Dec 5, 2025Dec 5, 2025

    • proBait

      Public
      Generate target-enrichment baits from a set of genome assemblies.
      Python
      •
      GNU General Public License v3.0
      •1•0•1•0•Updated Nov 28, 2025Nov 28, 2025

    • Schema_Refinery

      Public
      Set of scripts and instructions to refine wg/cgMLST schemas.
      Python
      •
      GNU General Public License v3.0
      •1•3•0•0•Updated Sep 12, 2025Sep 12, 2025

    • Chewie-NS_tutorial

      Public
      Python
      •
      GNU General Public License v3.0
      •0•0•0•3•Updated Sep 2, 2025Sep 2, 2025

    • Chewie-NS

      Public
      chewBBACA Nomenclature Server
      Python
      •
      GNU General Public License v3.0
      •0•7•1•13•Updated Jul 21, 2025Jul 21, 2025

    • seq_typing

      Public
      Determine which reference sequence is more likely to be present in a given sample
      Python
      •
      GNU General Public License v3.0
      •5•5•0•0•Updated Apr 15, 2025Apr 15, 2025

    • ReMatCh

      Public
      Reads mapping against target sequences, checking mapping and consensus sequences production
      C
      •
      GNU General Public License v3.0
      •5•8•2•0•Updated Apr 8, 2025Apr 8, 2025

    • ENA_microbial_submission

      Public
      Set of scripts and instructions to upload sequencing reads to the ENA.
      Python
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Aug 2, 2024Aug 2, 2024

    • docker-images

      Public
      Repository of Docker images created by UMMI
      Dockerfile
      •1•5•0•3•Updated Sep 29, 2023Sep 29, 2023

    • DEN-IM

      Public
      Dengue virus genotyping from shotgun and targeted metagenomics​ - A nextflow pipeline
      Python
      •
      GNU General Public License v3.0
      •5•7•3•0•Updated Apr 20, 2023Apr 20, 2023

    • long-read-catalog

      Public
      catalog for long-read sequencing tools
      10•32•0•0•Updated Feb 14, 2023Feb 14, 2023

    • LMAS

      Public
      LMAS - Last (Meta)Genomic Assembler Standing
      Python
      •
      GNU General Public License v3.0
      •2•11•1•1•Updated Dec 21, 2022Dec 21, 2022

    • INNUca

      Public
      INNUENDO quality control of reads, de novo assembly and contigs quality assessment, and possible contamination search
      Python
      •
      GNU General Public License v3.0
      •8•15•7•0•Updated Dec 14, 2022Dec 14, 2022

    • LMAS_Manuscript_Analysis

      Public
      HTML
      •0•0•0•0•Updated Aug 31, 2022Aug 31, 2022

    • LMAS.js

      Public
      Source code for the interactive report of LMAS workflow
      JavaScript
      •0•0•0•0•Updated Aug 24, 2022Aug 24, 2022

    • chewBBACA_tutorial

      Public
      Step by step tutorial using chewBBACA with all necessary files and results
      HTML
      •1•7•4•0•Updated Jun 28, 2021Jun 28, 2021

    • awesome-bioinfotools

      Public
      List of awesome resources for bioinformatics
      0•1•0•0•Updated Jan 27, 2021Jan 27, 2021

    • getSeqENA

      Public
      Get fastq files from ENA using Run IDs
      Python
      •
      GNU General Public License v3.0
      •3•1•1•1•Updated Sep 8, 2020Sep 8, 2020

    • Nomenclature_Server

      Public
      Python
      •1•0•0•0•Updated Nov 20, 2019Nov 20, 2019

    • INNUENDO_REST_API

      Public
      Frontend application and REST API for the INNUENDO Platform
      JavaScript
      •
      GNU General Public License v3.0
      •6•0•0•0•Updated Jun 25, 2019Jun 25, 2019

    • Online-PhyloViZ

      Public
      JavaScript
      •
      GNU General Public License v3.0
      •11•0•0•0•Updated Feb 18, 2019Feb 18, 2019

    • INNUENDO_PROCESS_CONTROLLER

      Public
      INNUENDO Process controller source code wiht integration with Nextflow
      Python
      •
      GNU General Public License v3.0
      •4•0•0•0•Updated Feb 4, 2019Feb 4, 2019

    • patho_typing

      Public
      In silico pathogenic typing directly from raw Illumina reads
      Python
      •
      GNU General Public License v3.0
      •1•4•0•1•Updated Jan 11, 2019Jan 11, 2019

    • INNUENDO_docker

      Public
      Docker-compose for INNUENDO Platform deployment
      Shell
      •
      GNU General Public License v3.0
      •9•0•0•0•Updated Jan 4, 2019Jan 4, 2019

    • pATLAS

      Public
      Plasmid Atlas - A web interface to browser for plasmids and their associated genes. Visit us at:
      JavaScript
      •
      GNU General Public License v3.0
      •8•1•0•0•Updated Nov 6, 2018Nov 6, 2018

    • Metagenomics-in-the-diagnostic-laboratory-workshop

      Public
      0•0•0•0•Updated Oct 19, 2018Oct 19, 2018

    • uBdbs-catalog

      Public
      useful bacterial databases catalog
      0•5•0•0•Updated Oct 14, 2018Oct 14, 2018

    • pATLASflow

      Public
      A pipeline to run mapping, mash screen and assembly methods for pATLAS.
      Python
      •
      GNU General Public License v3.0
      •2•0•0•0•Updated Sep 25, 2018Sep 25, 2018

    • Oneida_Genomics_Workshop

      Public
      4•0•0•0•Updated May 9, 2018May 9, 2018

    • ivrTyper

      Public
      ivr locus allele determination from genomic data
      C
      •2•0•0•0•Updated Jan 11, 2018Jan 11, 2018