Summary table

Key	Value
category	read-based/assembly-based
platform	illumina
open source	true
reproducible	true
documented	true

Database

This protocol uses Abricate v0.7 for detection of AMR genes in E. coli.

Protocol

• Step 1

Sequences were queried against the ResFinder database (2,228 sequences) and the CARD database (2,153 sequences) using ABRicate. The following parameters were used: % coverage ≥60, % identity ≥80 The RGI tool v4.0.3 by Jia et al., 2017 was used to confirm gene presence/absence, under “perfect” and “strict” match conditions.

• Step 2

De novo assembly was performed using the Shovill pipeline (v0.8.0).

Citation

The paper(s) documenting this protocol:

• Wang et al. Multi-Year Persistence of Verotoxigenic Escherichia coli (VTEC) in a Closed Canadian Beef Herd: A Cohort Study. Front Microbiol. 2018

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