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    19 repositories

    • 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

    • read-lab-confederation.github.io

      Public
      EMERGENT - EMory bactERial GEnomics aNd meTagenomics
      HTML
      •
      MIT License
      •0•0•0•0•Updated Feb 19, 2024Feb 19, 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/1-8TOA2eY1j5h5frcOCiKiCoTMN0JCwU3sVijJ-GvHSc/edit?usp=sharing
      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
      •2•3•1•0•Updated Jan 11, 2018Jan 11, 2018

    • staph_metagenome_subtypes

      Public
      HTML
      •2•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 other large genomes.
      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