Resources

AMR-Cap protocol

Allows detection of AMR genes.

travisg@uga.edu

No

Bactopia v3

Tools for the detection of antibiotic resistance (AMR) genes and mobile genetic elements (MGEs).

Complete analysis of bacterial genomes in one pipeline.

tread@emory.edu

Yes

Bactopia v3 Camlhmp Software (pbptyper)

A framework for creating, executing, and maintaining typing tools with simple, human-readable YAML files.

tread@emory.edu

Yes

Bactopia v3 Camlhmp Software (pasty)

tread@emory.edu

Yes

Bactopia v3 Camlhmp Software (sccmec)

tread@emory.edu

Yes

Bactopia v3 Camlhmp Software (tulatyper)

tread@emory.edu

Yes

CAPE analysis system

Infrastructure that can support the merging of multiple data streams including newly sequenced genomic data, clinical data, epidemiological data and surveillance data.

Data linkage; Reduction in people hours required to perform analyses.

Rebecca.Hutchins@gtri.gatech.edu

Yes

Curated Staphylococcus aureus pangenome

Curated dataset of substrains that represent the overall diversity of S. aureus.

Improved reference genome for S. aureus.

tread@emory.edu

Yes

HAI R script workflow

Automates data structuring, linkage, analysis. Applies to subset of pathogens tracked through ABCs (EIP), ARLN.

Faster, easier, greater accuracy.

Rebecca.Hutchins@gtri.gatech.edu

Yes

Influenza-like Illness

Explores associations between regional summaries of local commuting patterns and regional influenza-like illness (ILI) epidemics using regression models.

Heterogeneity in mobility / population mixing at smaller spatial scales has often been ignored / assumed uniform or negligible; this shows information at finer / more granular spatial resolutions can be effectively translated to explain variation at coarser spatial resolutions.

justin.bahl@uga.edu

Yes

Influenza-like Illness clustering

Identifies spatial and commuting network clusters (groups of states) with similar patterns in the incidence of Influenza like illness data.

Clustering patterns can inform risk assessments and help to define proximal "transmission zones."

justin.bahl@uga.edu

Yes

Joint Estimation

Analytical workflows that trace imported SARS-CoV-2 clusters using large-scale genome datasets. These approaches pinpoint when, where, and how many introductions occurred, while tracking the circulation of resulting clusters.

Rapid molecular epidemiology inference to help track SARS-CoV-2 transmission in near-real time.

justin.bahl@uga.edu

Yes

Joint Estimation

Incorporating metrics such as Source Sink Score, Local Import Score, and Persistence Time, analyses reveal transmission heterogeneity between subregions of focal area.

justin.bahl@uga.edu

Yes

Metagenomic analysis pipeline

This pipeline consists of a series of individual scripts that perform various bioinformatics analyses, including read filtering, taxonomic classification, and BLAST searches. The pipeline is designed to process multiple samples in parallel.

Pathogen Agnostic analysis of clinical samples.

anne.piantadosi@emory.edu

Yes

Metagenomic sequencing protocol for respiratory virus detection and sequencing from negative SARS-CoV-2 RATs

Validated protocol for sample pooling, sequencing, and confirmation of positive results.

Expand genomic surveillance for respiratory viruses using self-collected samples.

anne.piantadosi@emory.edu

Yes

Mobility Models

The objective of this analysis is to characterize a "local" scale of human mobility within the US and explore its variability across larger regional scales.

Data-driven estimate (before defined arbitrarily) of "local" spatial context that can be used to quantify population mixing applied to studies investigating pathogen transmission, outbreak investigations, or characterizing risk and spatial spread of infectious diseases.

justin.bahl@uga.edu

Yes

PathMIPs Co-seq method

This multiplex sequencing protocol sequences 3 viral respiratory pathogens simultaneously with molecular inversion probes & Oxford Nanopore sequencing. Allows 96 and up to 2000 samples in the same run.

Increased respiratory pathogen sequencing and surveillance capacity.

malabady@uga.edu

Yes

Phylogenetic Analysis Sampling Tool (PAST)

A tool which allows you to create a balanced and well-spread sample across an arbitrary number of relevant variables from a large population of sequences for subsequent phylogenetic analysis.

Increased representativeness, greater accuracy.

justin.bahl@uga.edu

Yes

Phylogeny and Metadata Network Database (PMeND)

Integrates any dataset, including genetic, ecological, and contact tracing network data, with sequence data for phylogenetic tree generation.

Scalable data integration.

justin.bahl@uga.edu

Yes

Seasonal Influenza Evolution

Characterize seasonal influenza transmission in context of local outbreaks.

Impossible to observe transmission using traditional epi methods (e.g. contact tracing) for the entire scope of outbreaks; genomic epi approaches can leverage information imprinted in pathogen genome to reveal these details.

justin.bahl@uga.edu

Yes

Spatial Structuring

Identifies a subnational regional delineation that optimally captures patterns in influenza epidemic dynamics, viral ancestry / inferred transmission, and human mobility.

Utility in policy (preparedness) and research, especially phylodynamics (eases computation and offers more valid spatial structure), as it defines proximal "influenza transmission zones."

justin.bahl@uga.edu

Yes

Spatial Transmission Count Statistic

The spatial transmission count statistic efficiently summarizes geographic transmission patterns imprinted in viral phylogenies. Guided by a time-scaled tree with ancestral trait states, we identified spatial transmission linkages and categorized them as imports, local transmissions, and exports.

Understand local-scale epidemic trends in near real-time of an outbreak.

justin.bahl@uga.edu

Yes

Subsamplerr

This R package processes case count tables and genome metadata, enabling visual exploration of sampling heterogeneity and the implementation of proportional sampling schemes.

Subsample genomic data based on epidemiological time series data.

justin.bahl@uga.edu

Yes

Tip-Trait Association Test (TTAT)

This R package provides analytical methods to decide if the association between tips of a phylogenic tree and traits (like genes or characteristics) is significant. By traversing the whole tree, this package provides functions highlighting all the subclades in which tips and characters are significantly associated.

Rapid molecular epidemiology inference to help flag key SARS-CoV-2 mutations in near-real time (short).

justin.bahl@uga.edu

Yes

Wastewater Genomic surveillance

Bayesian phylodynamic approaches to characterize SARS-CoV-2 variant dynamics using wastewater sequences.

Provides population-level coverage, capturing subclinical infections, and mitigates limited clinical testing.

justin.bahl@uga.edu

Yes

Wastewater sequencing protocol for SARS-CoV-2

This protocol describes how to prepare purified SARS-CoV-2 RNA from raw wastewater samples for short-read sequencing using a commercially available ARCTIC tiled amplicon panel.

elipp@uga.edu

Yes

iNextEra Library Preps v6(b)

Multiplexed short-read DNA libraries for whole-genome sequencing.

Cost conscious.

travisg@uga.edu

Yes