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. 2021 May 28;12:649517. doi: 10.3389/fmicb.2021.649517

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Copyright © 2021 Deneke, Uelze, Brendebach, Tausch and Malorny.

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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Schematic representation of the chewieSnake_join workflow. (A) A set of laboratories locally employ the chewieSnake workflow to process incoming raw sequencing data. The resulting allele profiles are stored in individual allele databases, which are subsequently joined with the chewieSnake_join workflow. In addition, the chewieSnake_join workflow computes a joined cgMLST report. (B) Detailed description of the chewieSnake_join workflow. From the joined allele profiles, the allele distance matrix is computed, followed by cluster typing of the entire dataset. Detailed reports for each cluster as well as an overall report summarize the results in an interactive HTML format.