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    20 repositories

    • read-lab-confederation.github.io

      Public
      EMERGENT - EMory bactERial GEnomics aNd meTagenomics
      HTML
      •
      MIT License
      •0•0•0•0•Updated Jul 24, 2026Jul 24, 2026

    • kmer-diff

      Public
      Python
      •0•0•0•0•Updated Jul 20, 2026Jul 20, 2026

    • lab_hackathon2

      Public
      Our project is to adapt Brooke's script for determining AMR reads per million from meta genomic data
      Python
      •
      MIT License
      •0•0•1•0•Updated May 13, 2024May 13, 2024

    • github-collab-practice

      Public
      For practicing github commands with collaborators
      0•0•0•0•Updated Jun 29, 2023Jun 29, 2023

    • emergent-metagenome-pipeline

      Public
      A pipeline written in nextflow for processing metagenomes and identifying sequences within metagenomes
      Shell
      •0•0•0•0•Updated Jun 21, 2023Jun 21, 2023

    • antibiograms

      Public
      Data and script for parsing BioSample antibiogram data
      Creative Commons Zero v1.0 Universal
      •0•0•0•0•Updated May 8, 2023May 8, 2023

    • Ct_MAP_analysis

      Public
      HTML
      •0•0•0•0•Updated Jan 22, 2023Jan 22, 2023

    • panplots

      Public
      A small R script for generating pangenome accumulation curves
      R
      •2•0•0•0•Updated Apr 2, 2022Apr 2, 2022

    • hAMRoaster

      Public
      hAMRoaster is an analysis pipeline that can compare the output of nine different tools for detecting AMR genes and provide metrics of their performance
      Python
      •
      Creative Commons Zero v1.0 Universal
      •3•0•0•0•Updated Feb 9, 2022Feb 9, 2022

    • MRSA_bloodstream_clusters

      Public
      2018-2019 Genomic Clusters of bacteremia associated with MRSA
      0•1•0•0•Updated Dec 23, 2021Dec 23, 2021

    • Saureus_short_seq_database

      Public
      Creating fasta file for the database of short DNA sequences from S. aureus publications https://docs.google.com/spreadsheets/d/1-8TOA2eY1j5h5frcOCiKiCoTMN0JCwU3…
      R
      •0•0•0•0•Updated Mar 19, 2021Mar 19, 2021

    • gaeip-nthi

      Public
      Genomic analysis of nontypeable Haemophilus influenzae samples from Georgia Emerging Infections Program surveillance.
      HTML
      •
      MIT License
      •0•0•0•0•Updated Mar 19, 2021Mar 19, 2021

    • emergent-website

      Public archive
      Development repository for the EMERGENT website
      HTML
      •
      MIT License
      •0•0•0•0•Updated Feb 28, 2021Feb 28, 2021

    • supernova-16s

      Public
      Analysis of the Supernova 16S data set.
      HTML
      •
      MIT License
      •0•1•0•0•Updated Aug 1, 2019Aug 1, 2019

    • nyc-subway-anthrax-study

      Public
      Searching for anthrax in the New York City subway metagenome.
      Shell
      •
      MIT License
      •3•3•1•0•Updated Jan 11, 2018Jan 11, 2018

    • staph_metagenome_subtypes

      Public
      HTML
      •3•1•0•0•Updated Jan 8, 2017Jan 8, 2017

    • Whale_shark_v1

      Public
      How the first version of the whale shark genome assemblies was processed to remove contaminants. Might be of interest for others handling the same problems for …
      Makefile
      •
      MIT License
      •0•0•0•0•Updated Mar 19, 2016Mar 19, 2016

    • whaleshark

      Public
      Draft sequencing and assembly of the genome of the world’s largest fish, the whale shark: Rhincodon typus
      Shell
      •0•0•0•0•Updated Jan 11, 2015Jan 11, 2015

    • Neisseria_gonorrhoea_Population_Study

      Public
      Python
      •0•0•0•0•Updated Nov 24, 2014Nov 24, 2014

    • papista-genome-sequencing

      Public
      Whole genome sequencing of Pandoraea apista using Oxford Nanopore MinION
      Shell
      •2•2•0•0•Updated Jul 11, 2014Jul 11, 2014
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