The Agilent Genomics NextGen Toolkit (AGeNT) is a Java-based software module that processes the read sequences from targeted high-throughput sequencing data generated by sequencing Agilent SureSelect and HaloPlex libraries. AGeNT trims low quality bases from the ends, removes adaptor sequences, and masks enzyme footprints (for HaloPlex). Properly curating read sequences prior to alignment improves alignment efficiency and decreases the rate of false positive variant calls. AGeNT also processes the Molecular Barcode (MBC) information in HaloPlexHS and SureSelect XT HS Illumina data, where it tags read pairs in a BAM/SAM file with their MBC sequences read out of the index 2 FASTQ file(s), and mark or remove MBC duplicates from that BAM/SAM file.

This module is the very same one that is used in the Agilent SureCall software package, which is offered as a desktop application for Windows and MacOS X systems.

DISCLAIMER: The Agilent Genomics NextGen Toolkit (AGeNT) module has been designed to provide the adaptor trimming and duplicate read removal capabilities of Agilent SureCall in a flexible command-line interface for integration into your bioinformatics pipeline. Agilent does not guarantee the usability of third party tools (open- or closed-source) in upstream/downstream analysis of data in conjunction with AGeNT. AGeNT is explicitly designed and fine-tuned for customers with established in-house bioinformatics experts with the capability to build, integrate, maintain, and troubleshoot internal analysis pipelines. Moreover, the module is designed specifically for customers with sufficient computing infrastructure and IT support to troubleshoot all issues unrelated to the execution of the AgeNT algorithms. Because Agilent provides limited support of AGeNT, we encourage users without thorough bioinformatics expertise to use Agilent SureCall software instead.

For Research Use Only. Not for use in diagnostic procedures.