Software and Tools
Software and tools developed as part of the GRDI-AMR1|2 projects.
Acheron
Acheron is a command line based workflow manager that allows for large scale, fast, and memory efficient machine-learning analyses of whole-genome sequence data.
BaitCapture
BaitCapture is a bioinformatics workflow designed for processing sequencing data obtained from targeted resistome bait-capture sequencing, built using Nextflow.
ConFindr
ConFindr is designed to find bacterial intra-species contamination in raw Illumina data.
DataHarmonizer
DataHarmonizer is a standardized browser-based spreadsheet editor and validator, which works off of LinkML data specifications.
GRDI-AMR Data Specification
The GRDI-AMR Data Specification for harmonizing One Health AMR pathogen genomics contextual data.
MOB-suite
MOB-suite is a group of software tools for clustering, reconstruction and typing of plasmids from draft assemblies.
staramr
staramr (*AMR) scans bacterial genome contigs against the ResFinder, PointFinder, and PlasmidFinder databases and compiles a summary report of detected antimicrobial resistance genes.