AMR Benchmarking dataset - Mapped ReadSets - 1

Benchmarking dataset for AMR detection pipelines for assemblies focusing on ESKAPE pathogens in addition to Salmonella. This dataset consists of closed genomes from NCBI where paired-end Illumina data was available. The closed genomes from NCBI are provided in addition to assemblies based on the raw uploaded to NCBI, along with assemblies based on just the reads which mapped correctly to the closed assemblies. Reads were assembled using shovill v. 1.1.0 using SKESA and SPADES.  Variants were called using snippy v. 4.6.0 and the mapped reads were extracted bedtools bamtofastq v2.29.2.