Bacterial Whole Genome Sequencing and Assembly

Bacterial DNA was extracted and whole genomes were sequenced by Illumina HiSeq X platform at SciLifeLab (Stockholm, Sweden) and Ion Torrent S5 XL platform (Thermo Fisher Scientific, Waltham, Massachusetts, US) at The Public Health Agency of Sweden as previously described [26 ]. The Illumina sequencing reads were de novo assembled with SKESA (version 2.3.0) [27 (link)]. The Ion Torrent sequencing reads were de novo assembled with SPAdes (version 3.12.0) in “careful mode” [28 (link)]. The genome assemblies were annotated with Prokka (version 1.14.6) [29 (link)]. The assemblies of all strains in this study were deposited in GenBank with accession numbers and metadata shown in Table S1.

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Hua Y., Bai X., Zhang J., Jernberg C., Chromek M., Hansson S., Frykman A., Yang X., Xiong Y., Wan C, & Matussek A. (2020). Molecular characteristics of eae-positive clinical Shiga toxin-producing Escherichia coli in Sweden. Emerging Microbes & Infections, 9(1), 2562-2570.

Publication 2020

HiSeq X platform Ion Torrent S5 XL platform

Bacterial dna Genome Strains

Corresponding Organization : University of Oslo

Other organizations : Massey University, Public Health Agency of Sweden, Karolinska University Hospital, Sahlgrenska University Hospital, University of Gothenburg

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Variable analysis

independent variables

Illumina HiSeq X platform
Ion Torrent S5 XL platform

dependent variables

Bacterial DNA extraction
Whole genome sequencing
De novo assembly of Illumina sequencing reads with SKESA
De novo assembly of Ion Torrent sequencing reads with SPAdes
Genome annotation with Prokka

control variables

Previously described [26]
Careful mode for SPAdes assembly

Annotations

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