Stars
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.
Comprehensive Antibiotic Resistance Probe Design Machine (CARPDM) for design of hybridization probes based on CARD reference sequences.
ARG normalization by mapping to the ARO ontology.
An international minimal metadata standard for public health and One Health genomic surveillance.
Organism-specific interpretation of AMR genotypes
Benchmark datasets for WGS analysis of SARS-CoV-2. (https://peerj.com/articles/13821/)
🦠 Huge collection of useful projects and resources for COVID-19 (2019 novel Coronavirus)
Tutorial notebooks and scripts for the mARG collection
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
PopPUNK 👨🎤 (POPulation Partitioning Using Nucleotide Kmers)
Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction
Differential topic analysis for molecular microbial data
Repository for suggesting new lineages that should be added to the current scheme
Collection of conceptual SVG figures created by me for talks
Software package for assigning SARS-CoV-2 genome sequences to global lineages.
Workflow to generate the shared orthologue network between input fastas e.g. plasmids
Multiple sequence alignment of SARS-CoV-2 genomes without homoplasic sites
Small collection of tools for performing quality control on coronavirus sequencing data and genomes
Supplemental code for "the architecture of SARS-CoV-2 transcriptome" paper
Visualization toolkit for SARS-CoV-2 whole genome sequencing data
Files and methodology pertaining to the sequencing and analysis of SARS-CoV-2, causative agent of COVID-19.