Comparison of quality performance of whole genome sequencing analysis pipelines for foodborne pathogens

Abstract: Campylobacter is the leading cause of gastroenteritis worldwide and in Sweden there areofficial programs for the surveillance of the bacteria. One important objective with foodbornepathogen surveillance is molecular typing. As typing based on whole genome sequencing datais becoming more common, knowledge on how to set up analysis pipelines is essential to avoidvariation in results. Here, typical whole genome sequencing pipelines are compared to areference genome at different analysis stages to optimize assembly quality and typing resultsusing cgMLST. The results show that read trimming is optimal to obtain high quality assemblieswith SPAdes as well as for improving cgMLST results compared to when no read trimming wasperformed before assembling with SPAdes. The opposite was shown for SKESA wheretrimming beforehand had negative effects on the results, most likely due to SKESA having builtin trimming properties. Additionally post assembly improvements had generally positive effects,however these effects were small.Tekni