PT  - JOURNAL ARTICLE
AU  - William Matlock
AU  - Samuel Lipworth
AU  - Bede Constantinides
AU  - Timothy E.A. Peto
AU  - A. Sarah Walker
AU  - Derrick Crook
AU  - Susan Hopkins
AU  - Liam P. Shaw
AU  - Nicole Stoesser
TI  - Flanker: a tool for comparative genomics of gene flanking regions
AID  - 10.1101/2021.02.22.432255
DP  - 2021 Jan 01
TA  - bioRxiv
PG  - 2021.02.22.432255
4099  - http://biorxiv.org/content/early/2021/02/22/2021.02.22.432255.short
4100  - http://biorxiv.org/content/early/2021/02/22/2021.02.22.432255.full
AB  - Analysing the flanking sequences surrounding genes of interest is often highly relevant to understanding the role of mobile genetic elements (MGEs) in horizontal gene transfer, particular for antimicrobial resistance genes. Here, we present Flanker, a Python package which performs alignment-free clustering of gene flanking sequences in a consistent format, allowing investigation of MGEs without prior knowledge of their structure. Flanker clusters flanking sequences based on Mash distances, allowing for easy comparison of similarity and the extent of this similarity across sequences. Additionally, Flanker can be flexibly parameterised to finetune outputs by characterising upstream and downstream regions separately and investigating variable lengths of flanking sequence. We apply Flanker to two recent datasets describing plasmid-associated carriage of important carbapenemase genes (blaOXA-48 and blaKPC-2/3) and show that it successfully identifies distinct clusters of flanking sequences (flank patterns), including both known and previously uncharacterised structural variants. We demonstrate that flank patterns are linked to geographical regions and carbapenem phenotypes, suggesting they may be useful as epidemiological markers. Flanker is freely available under an MIT license at https://github.com/wtmatlock/flanker.Data Summary NCBI accession numbers for all sequencing data used in this study is provided in Supplementary Table 1. The analysis performed in this manuscript can be reproduced in a binder environment provided on the Flanker Github page (https://github.com/wtmatlock/flanker).Competing Interest StatementThe authors have declared no competing interest.