Best Practices for SureSelect Data Processing

This guide outlines the best practices for processing raw sequencing data from SureSelect XT HS, XT HS2, Max, and Max MGI prior to variant discovery. The document details the necessary steps for pre-processing, which include removing sequencing adaptors, aligning processed reads to a reference genome, annotating aligned files with molecular barcode information, and performing PCR de-duplication. It recommends the use of AGeNT Trimmer and AGeNT CReaK tools for specific steps in the workflow. The guide also provides example commands for executing these processes on Linux or Mac systems, emphasizing the importance of using appropriate aligners such as BWA-MEM and STAR to ensure proper handling of molecular barcode tags. Additionally, it describes the generation of consensus reads and the options available for different consensus modes, ensuring that the output files are suitable for downstream analysis. The document is intended for research use only and is not for diagnostic or commercial applications.