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Genomic diversity affects the accuracy of bacterial SNP calling pipelines
[article]
2019
biorxiv/medrxiv
pre-print
Accurately identifying SNPs from bacterial sequencing data is an essential requirement for using genomics to track transmission and predict important phenotypes such as antimicrobial resistance. However, most previous performance evaluations of SNP calling have been restricted to eukaryotic (human) data. Additionally, bacterial SNP calling requires choosing an appropriate reference genome to align reads to, which, together with the bioinformatic pipeline, affects the accuracy and completeness
doi:10.1101/653774
fatcat:qkmibmufjrgtvnagptftntgv34