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    15 repositories

    • southeast-region

      Public
      Scripts, pipelines, and training materials for the AMD Southeast Region
      R
      •
      MIT License
      •1•4•0•0•Updated Oct 14, 2024Oct 14, 2024

    • docker-builds

      Public
      📦 🐳 Dockerfiles and documentation on tools for public health bioinformatics
      dockerbioinformaticscontainersdockerfilessingularity
      Dockerfile
      •
      GNU General Public License v3.0
      •119•187•32•12•Updated Oct 12, 2024Oct 12, 2024

    • staph-b.github.io

      Public
      Visit the site here: https://staphb.org
      SCSS
      •
      Other
      •1•7•0•1•Updated Aug 1, 2024Aug 1, 2024

    • staphb_toolkit

      Public
      Python Toolkit for using containerized programs in either Singularity or Docker
      Python
      •
      GNU General Public License v3.0
      •18•26•2•1•Updated Mar 19, 2024Mar 19, 2024

    • midwest-region

      Public
      Site for AMD Midwest Region
      CSS
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Feb 9, 2024Feb 9, 2024

    • central-region

      Public
      Site for AMD Central Region
      1•0•0•0•Updated Aug 23, 2023Aug 23, 2023

    • northeast-region

      Public
      HTML
      •0•1•0•3•Updated Apr 11, 2023Apr 11, 2023

    • mycosnp

      Public
      C. auris analysis workflow developed by the CDC translated for Nextflow
      Nextflow
      •0•1•0•0•Updated Feb 15, 2022Feb 15, 2022

    • titan

      Public archive
      Public health bioinformatics repository for WDL workflows to analyze viral genomes.
      WDL
      •
      GNU Affero General Public License v3.0
      •1•3•0•0•Updated Oct 19, 2021Oct 19, 2021

    • amd_academy_2020

      Public
      Resource for AMD Academy
      GNU General Public License v3.0
      •1•0•0•0•Updated Jun 18, 2020Jun 18, 2020

    • plasmadazz

      Public
      (In Development) - Plasmid searching and annotation tool for finished genome assemblies.
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Mar 4, 2020Mar 4, 2020

    • CDPHE

      Public
      Various pipelines and scripts used by the CO state public health lab
      Shell
      •
      GNU General Public License v3.0
      •4•2•2•0•Updated Jan 15, 2020Jan 15, 2020

    • resistanceDetectionCDC

      Public
      Shell
      •0•3•0•0•Updated Jul 17, 2019Jul 17, 2019

    • mountain-region

      Public
      BRR and WFD resource pages for the Mountain Region.
      0•0•0•0•Updated Jul 10, 2019Jul 10, 2019

    • BI_Implementation_Guide

      Public
      This document serves as a guide for State Public Health Laboratories considering hiring or working with bioinformaticians. It is currently under review with APHL and CDC.
      2•3•0•0•Updated Oct 15, 2018Oct 15, 2018