Amplicon sequencing is a powerful and cost effective method for sequencing a focused portion of the genome. This focused approach allows deep sequencing which is especially valuable in cancer samples. However, amplicon sequencing has many data characteristics which differ significantly from whole genome and hybridisation capture methods.
We have developed AmBiVErT (Amplicon Binning Variant caller with Error Trunctation), a software program that takes advantage of the features of amplicon sequencing and addresses the most common technical errors generated in amplicon assays. AmBiVErT uses alignment to reference amplicon sequences and a grouped read approach, binning redundant sequences and avoiding redundant calculation to provide rapid (<2 minutes for 1 million read pairs from 1000 amplicons) analysis of Illumina TruSeq amplicon, Agilent Haloplex and custom PCR amplicon data.
AmBiVErT is written in Python3 with C extensions and is available under the GPLv3 license.