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.