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    • Check if your reads have already been uploaded to NCBI
      Perl
      MIT License
      0000Updated Dec 5, 2024Dec 5, 2024
    • random scripts
      Python
      GNU General Public License v3.0
      0100Updated Nov 26, 2024Nov 26, 2024
    • bsProfile

      Public
      Make a bootstrap MLST tree from your profiles
      Perl
      MIT License
      0400Updated Nov 25, 2024Nov 25, 2024
    • An analysis pipeline for initial quality control and denoising of highly-multiplexed amplicon sequencing (HMAS) data, now without using mothur (as was used in the previous version)
      HTML
      MIT License
      2820Updated Oct 10, 2024Oct 10, 2024
    • ANI-paper

      Public
      Ruby
      0000Updated Oct 8, 2024Oct 8, 2024
    • datasets

      Public
      Benchmark and toy datasets
      Perl
      MIT License
      1590Updated Oct 2, 2024Oct 2, 2024
    • A Rosetta Stone for getting hashsums
      Python
      GNU General Public License v3.0
      0100Updated Sep 26, 2024Sep 26, 2024
    • Databases for wg/cgMLST analysis with the PN2.0 software
      11000Updated Sep 11, 2024Sep 11, 2024
    • tripod

      Public
      An analysis pipeline for checking the performance of stool_HMAS, isolate_HMAS, isolate_WGS data sets
      MIT License
      0000Updated Sep 9, 2024Sep 9, 2024
    • trapical

      Public
      trapical: trapical rapidly aligns Pulsenet islolate core alleles
      Python
      MIT License
      0400Updated Sep 5, 2024Sep 5, 2024
    • A pipeline for performing quality control on HMAS data, in preparation for downstream MLST-like or AMR-like analyses.
      Python
      2310Updated Aug 12, 2024Aug 12, 2024
    • Makes MD5sums with fewer bits using the Rust language
      Rust
      GNU General Public License v3.0
      0100Updated Jul 23, 2024Jul 23, 2024
    • Software to automatically call the espW allele in STEC genomes
      Python
      MIT License
      1000Updated Jun 20, 2024Jun 20, 2024
    • Latest Production Version of EDLB's version of Micropipe
      Nextflow
      GNU General Public License v3.0
      1000Updated May 20, 2024May 20, 2024
    • Python script(s) for assigning allele codes under current PulseNet nomenclature system in BioNumerics but as a command-line executable without BioNumerics dependencies
      Python
      3300Updated Apr 14, 2024Apr 14, 2024
    • R
      MIT License
      1101Updated Feb 2, 2024Feb 2, 2024
    • Ruby
      0000Updated Jan 25, 2024Jan 25, 2024
    • MIDAS2

      Public
      Metagenomic Intra-Species Diversity Analysis 2
      Python
      MIT License
      10100Updated Sep 26, 2023Sep 26, 2023
    • T3Pio

      Public
      Python
      2100Updated Jun 9, 2023Jun 9, 2023
    • Nextflow workflows created to address a variety of CDC-EDLB Nanopore sequencing bioinformatics needs
      Nextflow
      MIT License
      3000Updated Jun 6, 2023Jun 6, 2023
    • R
      0000Updated Sep 12, 2022Sep 12, 2022
    • This repository contains scripts and other documents pertaining to internal validation of the HMAS QC pipeline.
      Python
      1000Updated Apr 12, 2021Apr 12, 2021
    • Docker-compose for INNUENDO Platform deployment
      Shell
      GNU General Public License v3.0
      8000Updated Feb 3, 2021Feb 3, 2021
    • A collection of NCBI one-liners
      Shell
      MIT License
      0000Updated Oct 5, 2020Oct 5, 2020
    • Frontend application and REST API for the INNUENDO Platform
      JavaScript
      GNU General Public License v3.0
      5000Updated Aug 12, 2020Aug 12, 2020
    • repository for the INNUENDO chewbbaca schemas
      2000Updated Aug 12, 2020Aug 12, 2020
    • species specific training files based on specific reference genomes
      5000Updated Aug 12, 2020Aug 12, 2020