The corresponding metadata for the final isolates can be found can be found in data/strain.metadata.txt
- Genomic diversity affects the accuracy of bacterial single-nucleotide polymorphism–calling pipelines
- A comparison of tools for the simulation of genomic next-generation sequencing data
- Benchmarking bacterial genome-wide association study methods using simulated genomes and phenotypes
- A roadmap for the generation of benchmarking resources for antimicrobial resistance detection using next generation sequencing
- Benchmark datasets for phylogenomic pipeline validation, applications for foodborne pathogen surveillance
- MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies —see Supplentary File 2
- Simulation code for metagenomics including random copy number and insertion of AMR genes (either in a slightly painful seqan based C++ implementation or a simple nextflow workflow.): https://github.com/fmaguire/metagenome_simulator
- https://github.com/CAMI-challenge/CAMISIM: more of a proper taxonomic simulator (i.e., can use 16S taxonomic profiles to simulate the metagenome) but doesn't handle being able to insert/label AMR genes.
- FDA-ARGOS bioproject : https://www.ncbi.nlm.nih.gov/bioproject/231221
- https://github.com/metagenlab/MeSS: workflow to simulate metagenomic datasets from published genomes
- https://www.jpiamr.eu/projects/seq4amr/
- https://academic.oup.com/gigascience/pages/data_note
- https://github.com/phac-nml/staramr/blob/master/staramr/databases/resistance/data/ARG_drug_key_resfinder.tsv
- https://github.com/tseemann/injecta : Insert genes into genomes to aid synthetic test data generation