AGeNT

An 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 cuts low-quality bases from the ends remove adaptor sequences, and masks enzyme footprints (for HaloPlex).

AGeNT processes the Molecular Barcode (MBC) information in HaloPlexHS and

SureSelectXT HS Illumina data. AGeNT 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.