Summary

category	assembly-based
platform	illumina
open source	true
reproducible	true
documented	true

Database

This protocol uses the ARG-ANNOT database as curated by the SRST2. Not completely clear which file of the several ARG-ANNOT databases provided on the site that was used.

Protocol

• Step 1 - Trimming

Trimming using trimmomatic1.32

• Step 2 - Assembly

Assembly done using SPAdes-3.0.0

• Step 3 - AMR detection

Detection using blastn-2.4.0 Criteria: ≥50% coverage and ≥75% nucleotide identity

Citation

The paper(s) documenting this protocol:

• Carroll et. al.. Whole-Genome Sequencing of Drug-Resistant Salmonella enterica Isolates from Dairy Cattle and Humans in New York and Washington States Reveals Source and Geographic Associations

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