Clinical bioinformatics plays a key role in the implementation of clinical next-generation sequencing (NGS) testing infrastructure. Bioinformatics workflows in a clinical laboratory are complex and therefore need to be validated as part of an end-to-end NGS assay validation before clinical use. The validation cohort should be representative of the types of samples, types of variants, lower limits of detection of the assay, as well as sequence context of the panel. When validating an NGS bioinformatics pipeline, the pipeline validation lifecycle should be adhered to. Software containers and modern software automation tools can allow the building of a scalable and reliable clinical bioinformatics infrastructure and can be implemented in clinical bioinformatics operations in a phased way depending on the size and skillset of the bioinformatics team.