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. 2019 Sep 24;7(10):388. doi: 10.3390/microorganisms7100388

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© 2019 by the authors.

Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).

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Schematic bioinformatics data processing workflows for whole-genome sequence analysis. Left: alignment/mapping-based analysis. Multi-locus sequence typing (MLST) is based on species determination, while the reference genome is selected based on both species and MLST uncovered. Right: k-mer-based analysis. Contigs cleaning is optional, mainly for those isolates with an outstanding size of the assembled “genome”. SNVs: single nucleotide variants; ARGs: antibiotic resistance genes; VFs: virulence factors.