{"references": ["Fursova NK, Astashkin EI, Ershova ON, Aleksandrova IA, Savin IA, Novikova TS, et al. Multidrug-Resistant Klebsiella pneumoniae Causing Severe Infections in the Neuro-ICU. Antibiotics (Basel). 2021 August 13", "Jansson M\u00f6rk M, Karamehmedovic N, Hansen A, Nederby \u00d6hd J, Lindblad M, \u00d6stlund E, et al. Outbreak of Salmonella Newport linked to imported frozen cooked crayfish in dill brine, Sweden, July to November 2019. Eurosurveillance. 2022 June: p. 2.", "Wang LYR, Jokinen CC, Laing CR, Johnson RP, Ziebell K, Gannon VPJ. Assessing the genomic relatedness and evolutionary rates of persistent verotoxigenic Escherichia coli serotypes within a closed beef herd in Canada. Microbial Genomics. 2020 June 3: p. e000376.", "Spanelova P, Jakubu V, Malisova L, Musilek M, Kozakova J, Papagiannitsis CC, et al. Whole genome sequencing of macrolide resistant Streptococcus pneumoniae serotype 19A sequence type 416. BMC Microbiology. 2020 July 25."]}

Input data: 20230914-data-overview.xlsx: mapping of placeholder sample numbers to original SRA accession numbers 1199234567-*.fastq.gz: renamed Illumina MiSeq reads; reads for 1199234567-5 have been obtained by downsampling SRR10955980 madsdata: LIS report and bacteria list used for LIS-specific results Expected results: Results of the RSYD-BASIC pipeline, version 1.8.0, with the test dataset