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    • Set of scripts and instructions to refine wg/cgMLST schemas.
      Python
      Other
      1300Updated Dec 23, 2024Dec 23, 2024
    • chewBBACA

      Public
      BSR-Based Allele Calling Algorithm
      HTML
      GNU General Public License v3.0
      28138172Updated Nov 5, 2024Nov 5, 2024
    • Set of scripts and instructions to upload sequencing reads to the ENA.
      Python
      GNU General Public License v3.0
      0000Updated Aug 2, 2024Aug 2, 2024
    • proBait

      Public
      Generate target-enrichment baits from a set of genome assemblies.
      Python
      GNU General Public License v3.0
      1000Updated May 20, 2024May 20, 2024
    • Chewie-NS

      Public
      chewBBACA Nomenclature Server
      Python
      GNU General Public License v3.0
      17013Updated Nov 3, 2023Nov 3, 2023
    • Repository of Docker images created by UMMI
      Dockerfile
      1503Updated Sep 29, 2023Sep 29, 2023
    • Determine which reference sequence is more likely to be present in a given sample
      Python
      GNU General Public License v3.0
      4520Updated Aug 21, 2023Aug 21, 2023
    • DEN-IM

      Public
      Dengue virus genotyping from shotgun and targeted metagenomics​ - A nextflow pipeline
      Python
      GNU General Public License v3.0
      5730Updated Apr 20, 2023Apr 20, 2023
    • catalog for long-read sequencing tools
      113200Updated Feb 14, 2023Feb 14, 2023
    • Python
      GNU General Public License v3.0
      0003Updated Feb 2, 2023Feb 2, 2023
    • LMAS

      Public
      LMAS - Last (Meta)Genomic Assembler Standing
      Python
      GNU General Public License v3.0
      21011Updated 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
      71370Updated Dec 14, 2022Dec 14, 2022
    • ReMatCh

      Public
      Reads mapping against target sequences, checking mapping and consensus sequences production
      C
      GNU General Public License v3.0
      6821Updated Dec 14, 2022Dec 14, 2022
    • HTML
      0000Updated Aug 31, 2022Aug 31, 2022
    • LMAS.js

      Public
      Source code for the interactive report of LMAS workflow
      JavaScript
      0000Updated Aug 24, 2022Aug 24, 2022
    • Step by step tutorial using chewBBACA with all necessary files and results
      HTML
      1740Updated Jun 28, 2021Jun 28, 2021
    • List of awesome resources for bioinformatics
      0100Updated Jan 27, 2021Jan 27, 2021
    • getSeqENA

      Public
      Get fastq files from ENA using Run IDs
      Python
      GNU General Public License v3.0
      3111Updated Sep 8, 2020Sep 8, 2020
    • Python
      1000Updated Nov 20, 2019Nov 20, 2019
    • Frontend application and REST API for the INNUENDO Platform
      JavaScript
      GNU General Public License v3.0
      5000Updated Jun 25, 2019Jun 25, 2019
    • JavaScript
      GNU General Public License v3.0
      11000Updated Feb 18, 2019Feb 18, 2019
    • INNUENDO Process controller source code wiht integration with Nextflow
      Python
      GNU General Public License v3.0
      4000Updated Feb 4, 2019Feb 4, 2019
    • In silico pathogenic typing directly from raw Illumina reads
      Python
      GNU General Public License v3.0
      1401Updated Jan 11, 2019Jan 11, 2019
    • Docker-compose for INNUENDO Platform deployment
      Shell
      GNU General Public License v3.0
      8000Updated 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
      10100Updated Nov 6, 2018Nov 6, 2018
    • 0000Updated Oct 19, 2018Oct 19, 2018
    • useful bacterial databases catalog
      0500Updated Oct 14, 2018Oct 14, 2018
    • A pipeline to run mapping, mash screen and assembly methods for pATLAS.
      Python
      GNU General Public License v3.0
      2000Updated Sep 25, 2018Sep 25, 2018
    • 4000Updated May 9, 2018May 9, 2018
    • ivrTyper

      Public
      ivr locus allele determination from genomic data
      C
      2000Updated Jan 11, 2018Jan 11, 2018