Repository for suggesting new lineages that should be added to the current scheme

ARG normalization by mapping to the ARO ontology.

Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction

Analyzing CARD:Epi data via a Confusogram and UMAP.

Files and methodology pertaining to the sequencing and analysis of SARS-CoV-2, causative agent of COVID-19.

Software package for assigning SARS-CoV-2 genome sequences to global lineages.

🔎 💊 Mass screening of contigs for antimicrobial and virulence genes

This is the webpage of the ESGEM-AMR Working Group

AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.

IRIDA Plugin for AMR Detection

🆔 Scan contig files against PubMLST typing schemes

Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on homology and SNP models.

Organism-specific interpretation of AMR genotypes

Tiling PCR primer scheme definitions

PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)

The eskape model standalone application for eskape.mcmaster.ca

Python utilities for Manubot: Manuscripts, open and automated

Collection of conceptual SVG figures created by me for talks

The Mobilome Ontology describes bacterial mobile genetic elements, their mechanisms, and associated epidemiology.

The Antibiotic Resistance Ontology (ARO) organizes the information describing the ability of a microorganism to withstand the effects of an antibiotic. It reflects the latest curation at CARD.

The next major phase of ARO development has begun, addressing issues of orthogonality and fundamental ontological design. ARO Next development is independent of ongoing curation at CARD.

CARD's draft Virulence Ontology (VIRO) describing bacterial virulence

Comprehensive Antibiotic Resistance Probe Design Machine (CARPDM) for design of hybridization probes based on CARD reference sequences.

A public repository for collective curation of antimicrobial resistance (AMR) genes and mutations. Submit, discuss, and resolve AMR curation issues.

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies

Harmonization of AMR predictor tool outputs

🦠 Huge collection of useful projects and resources for COVID-19 (2019 novel Coronavirus)