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antibiograms

Data and script for parsing BioSample antibiogram data

ct_map_analysis

emergent-metagenome-pipeline

A pipeline written in nextflow for processing metagenomes and identifying sequences within metagenomes

emergent-website

Development repository for the EMERGENT website

github-collab-practice

For practicing github commands with collaborators

hamroaster

hAMRoaster is an analysis pipeline that can compare the output of nine different tools for detecting AMR genes and provide metrics of their performance

lab_hackathon2

Our project is to adapt Brooke's script for determining AMR reads per million from meta genomic data

mrsa_bloodstream_clusters

2018-2019 Genomic Clusters of bacteremia associated with MRSA

neisseria_gonorrhoea_population_study

nyc-subway-anthrax-study

Searching for anthrax in the New York City subway metagenome.

panplots

A small R script for generating pangenome accumulation curves

papista-genome-sequencing

Whole genome sequencing of Pandoraea apista using Oxford Nanopore MinION

read-lab-confederation.github.io

EMERGENT - EMory bactERial GEnomics aNd meTagenomics

saureus_short_seq_database

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

staph_metagenome_subtypes

supernova-16s

Analysis of the Supernova 16S data set.

whale_shark_v1

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.

whaleshark

Draft sequencing and assembly of the genome of the world’s largest fish, the whale shark: Rhincodon typus