Illumina NextSeq500 Whole Genome Sequencing

Nextera XT libraries were prepared for each of the samples. The barcoded libraries were pooled into equimolar concentrations following manufacturer’s guidelines (Illumina, San Diego, CA) using the Mid-Output Kit for paired-end sequencing (2×150 bp) on an Illumina NextSeq500 sequencing platform. Raw data (mean virtual coverage 361x) was demultiplexed and subsequently clipped of adapters using Trimmomatic v0.38 with default parameters^{46 (link)}. Quality control passing read-pairs were aligned against reference genome/plasmids (Accession numbers: NC_016810.1, NC_017718.1, NC_017719.1, NC_017720.1) with bwa v0.7.17^{47 (link)}. Genomic variant were called using Pilon v1.23 ^{48 (link)}. with the following parameters: (i) minimum coverage 10x; (ii) minimum quality score = 20; (iii) minimum read mapping quality = 10. SnpEff v4.3 was used to annotate variants according to NCBI and predict their effect on genes^{49 (link)}.

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Diard M., Bakkeren E., Lentsch V., Rocker A., Bekele N.A., Hoces D., Aslani S., Arnoldini M., Böhi F., Schumann-Moor K., Adamcik J., Piccoli L., Lanzavecchia A., Stadtmueller B.M., Donohue N., van der Woude M.W., Hockenberry A., Viollier P.H., Falquet L., Wüthrich D., Bonfiglio F., Loverdo C., Egli A., Zandomeneghi G., Mezzenga R., Holst O., Meier B.H., Hardt W.D, & Slack E. (2021). A rationally designed oral vaccine induces Immunoglobulin A in the murine gut that directs the evolution of attenuated Salmonella variants. Nature microbiology, 6(7), 830-841.

Publication 2021

Mid-Output Kit NextSeq500 sequencing platform

Genomic Plasmids

Corresponding Organization : ETH Zurich

Other organizations : University of Oxford, University of Zurich, University Hospital of Zurich, Università della Svizzera italiana, University of Illinois Urbana-Champaign, Medical University of Graz, Hull York Medical School, University of York, Swiss Federal Institute of Aquatic Science and Technology, University of Geneva, University of Fribourg, SIB Swiss Institute of Bioinformatics, University Hospital of Basel, Research Center Borstel - Leibniz Lung Center

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Variable analysis

independent variables

Nextera XT libraries preparation for each sample

dependent variables

Genomic variants called using Pilon v1.23

control variables

Minimum coverage 10x
Minimum quality score = 20
Minimum read mapping quality = 10

controls

No positive or negative controls were explicitly mentioned.

Annotations

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