Computational protocol: Clinical Isolates of Shiga Toxin 1a–Producing Shigella flexneri with an Epidemiological Link to Recent Travel to Hispañiola

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Protocol publication

[…] DNA was isolated from overnight cultures by using a QIAGEN DNEasy Kit (Valencia, CA, USA). Samples were prepared for sequencing by using a Nextera XT DNA Sample Preparation Kit (Illumina, San Diego, CA, USA) and sequenced on an Illumina MiSeq sequencing system. The phage sequence was assembled by mapping the reads to the reference phage NC_004913.2 by using Bowtie 2 version 2.1.0 (http://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.1.0/). […]

Pipeline specifications

Software tools Bowtie, Bowtie2
Application WGS analysis
Organisms Shigella flexneri, Homo sapiens, Shigella dysenteriae, Escherichia coli
Diseases Intestinal Diseases, Drug-Related Side Effects and Adverse Reactions
Chemicals Mitomycin