![]() ![]() ![]() Sequence logos (44) were created with the online program WebLogo. Conservation scores were calculated by the same method as by ClustalW2 (by dividing the number of identities in the best alignment by the number of residues compared). However, implementation of high-quality NGS and bioinformatics in research and public health laboratories can be challenging.įor instance, NGS and bioinformatics approaches have been used to identify outbreak origins, track transmissions, investigate epidemic dynamics, determine etiological agents of a disease, and discover novel human pathogens. Sequence alignment gures and phylogeny tree depictions were generated using CLC Sequence Viewer version 5.0.1. These challenges mainly include the choice of the sequencing platform and the sequencing approach, the choice of bioinformatics methodologies, access to the appropriate computation and information technology infrastructure, and recruiting and retaining personnel with the specialized skills and experience in this field. In this review, we summarize the most common NGS and bioinformatics workflows in the context of infectious disease genomic surveillance and pathogen discovery, and highlight the main challenges and considerations for setting up an NGS and bioinformatics-focused infectious disease research public health laboratory. We describe the most commonly used sequencing platforms and review their strengths and weaknesses. We review sequencing approaches that have been used for various pathogens and study questions, as well as the most common difficulties associated with these approaches that should be considered when implementing in a public health or research setting. ![]()
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