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    32 repositories

    • stylo

      Public
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Aug 21, 2025Aug 21, 2025

    • HMAS-QC-Pipeline2

      Public
      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
      •3•9•2•0•Updated Aug 12, 2025Aug 12, 2025

    • HMAS-QC-Pipeline

      Public
      A pipeline for performing quality control on HMAS data, in preparation for downstream MLST-like or AMR-like analyses.
      Python
      •3•3•1•0•Updated Aug 7, 2025Aug 7, 2025

    • basespace_automation

      Public
      scripts for automatic downloading fastq.gz files from basespace account and kick off step_mothur pipeline
      Python
      •
      MIT License
      •0•0•0•0•Updated Jul 16, 2025Jul 16, 2025

    • docker-builds

      Public
      📦 🐳 Dockerfiles and documentation on tools for public health bioinformatics
      Dockerfile
      •
      GNU General Public License v3.0
      •134•0•0•0•Updated Jun 30, 2025Jun 30, 2025

    • MatrixCodes

      Public
      Script to assign hierarchical nomenclature to samples present in a distance matrix, using user-defined thresholds in a single-linkage framework
      Python
      •0•2•0•0•Updated May 22, 2025May 22, 2025

    • BIOME-scripts

      Public
      random scripts
      Python
      •
      GNU General Public License v3.0
      •1•2•0•0•Updated May 21, 2025May 21, 2025

    • tripod

      Public
      An analysis pipeline for checking the performance of stool_HMAS, isolate_HMAS, isolate_WGS data sets
      MIT License
      •0•0•0•0•Updated Mar 18, 2025Mar 18, 2025

    • espwAlleleCaller

      Public
      Software to automatically call the espW allele in STEC genomes
      Python
      •
      MIT License
      •2•1•0•0•Updated Jan 30, 2025Jan 30, 2025

    • ontMetagenomics

      Public
      Metagenomics for ONT data
      Shell
      •
      MIT License
      •1•0•0•0•Updated Jan 22, 2025Jan 22, 2025

    • datasets

      Public
      Benchmark and toy datasets
      Perl
      •
      MIT License
      •3•11•9•0•Updated Jan 8, 2025Jan 8, 2025

    • checkSraIfUploaded

      Public
      Check if your reads have already been uploaded to NCBI
      Perl
      •
      MIT License
      •1•0•0•0•Updated Jan 8, 2025Jan 8, 2025

    • bsProfile

      Public
      Make a bootstrap MLST tree from your profiles
      Perl
      •
      MIT License
      •1•4•0•0•Updated Nov 25, 2024Nov 25, 2024

    • ANI-paper

      Public
      Ruby
      •1•0•0•0•Updated Oct 8, 2024Oct 8, 2024

    • hash_sequence

      Public
      A Rosetta Stone for getting hashsums
      Python
      •
      GNU General Public License v3.0
      •1•1•0•0•Updated Sep 26, 2024Sep 26, 2024

    • pn2.0-mlst-databases

      Public
      Databases for wg/cgMLST analysis with the PN2.0 software
      2•10•0•0•Updated Sep 11, 2024Sep 11, 2024

    • trapical

      Public
      trapical: trapical rapidly aligns Pulsenet islolate core alleles
      Python
      •
      MIT License
      •1•4•0•0•Updated Sep 5, 2024Sep 5, 2024

    • md5_reducer

      Public
      Makes MD5sums with fewer bits using the Rust language
      Rust
      •
      GNU General Public License v3.0
      •1•1•0•0•Updated Jul 23, 2024Jul 23, 2024

    • EDLB-micropipe-LATEST

      Public
      Latest Production Version of EDLB's version of Micropipe
      Nextflow
      •
      GNU General Public License v3.0
      •2•0•0•0•Updated May 20, 2024May 20, 2024

    • AlleleCodes

      Public
      Python script(s) for assigning allele codes under current PulseNet nomenclature system in BioNumerics but as a command-line executable without BioNumerics dependencies
      Python
      •4•3•0•0•Updated Apr 14, 2024Apr 14, 2024

    • source-attribution-MLST

      Public
      R
      •
      MIT License
      •2•1•0•1•Updated Feb 2, 2024Feb 2, 2024

    • ncezid-biome.github.io

      Public
      Ruby
      •1•0•0•0•Updated Jan 25, 2024Jan 25, 2024

    • MIDAS2

      Public
      Metagenomic Intra-Species Diversity Analysis 2
      Python
      •
      MIT License
      •12•1•0•0•Updated Sep 26, 2023Sep 26, 2023

    • T3Pio

      Public
      Python
      •3•1•0•0•Updated Jun 9, 2023Jun 9, 2023

    • nanoporeWorkflow

      Public
      Nextflow workflows created to address a variety of CDC-EDLB Nanopore sequencing bioinformatics needs
      Nextflow
      •
      MIT License
      •4•0•0•0•Updated Jun 6, 2023Jun 6, 2023

    • NGSU_LibPrep_2021

      Public
      R
      •1•0•0•0•Updated Sep 12, 2022Sep 12, 2022

    • HMAS-Internal-Validation

      Public
      This repository contains scripts and other documents pertaining to internal validation of the HMAS QC pipeline.
      Python
      •2•0•0•0•Updated Apr 12, 2021Apr 12, 2021

    • INNUENDO_docker

      Public
      Docker-compose for INNUENDO Platform deployment
      Shell
      •
      GNU General Public License v3.0
      •9•0•0•0•Updated Feb 3, 2021Feb 3, 2021

    • ncbi-one-liners

      Public
      A collection of NCBI one-liners
      Shell
      •
      MIT License
      •1•0•0•0•Updated Oct 5, 2020Oct 5, 2020

    • 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 Aug 12, 2020Aug 12, 2020