Candida auris sequencing by Illumina miSeq using Illumina DNA Prep v1

Candida auris sequencing is becoming more important for public health and surveillance. This protocol is designed to guide individuals experienced in sequencing in setting up a SOP for sequencing C. auris. This protocol is designed for Illumina short-read sequencing. While the miSeq is the described instrument it is generally not difficult to scale up or down to other instruments. We have not validated using 150x150 read lengths. The DNA prep kit is the recommended kit. The NexteraXT kit produces varying fragment sizes across samples and usually results in lower coverage and sequencing quality than samples prepared with DNA Prep. This does not include bioinformatic analysis- however you can contact the author for more information.