Assessing the impact of sequencing platforms and analytical pipelines on whole-exome sequencing

As the demand for WES increases and the cost of NGS decreases, WES, as a technique, requires a generous understanding of how experimental design can improve data interpretation and thus improve biological outcomes. In this study, tumor standard HD832 and normal sample HG001 were used. NovaSeq 6000, NextSeq 550, GenoLab M, FASTASeq 300 and SURFSeq 5000 sequencing platforms were used. Comparing the performance of SNP and InDel in various sequencing platforms and analysis software, it was found that sequencing platform had little impact on the results of whole exome sequencing (WES), while analysis software had more impact on the results of WES. In addition, the importance of biological replication for WES testing is also emphasized. Through the comparative analysis of multiple data sets, it was found that for HD832 and HG001 samples, analysis software had a greater impact on WES results than sequencing platform.

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