AmpliSolve

AmpliSolve is a bioinformatics tool to detect low-frequency single nucleotide variants (SNVs) in targeted deep sequencing data, particularly for amplicon-based libraries sequenced with the Ion Torrent platform. The tool addresses the challenge of high noise levels in this data type by modeling position-specific, strand-specific, and nucleotide-specific background artifacts using a set of normal samples.

AmpliSolve employs a Poisson model-based statistical framework for SNV detection, enabling it to balance precision and sensitivity well, even at variant allele frequencies (VAFs) below 5% and as low as 1%. The tool's performance has been validated using both synthetic and real data and through comparison with digital droplet PCR experiments for detecting SNVs in circulating tumor DNA samples. Although primarily designed for the Ion Torrent platform, AmpliSolve can also be applied to other sequencing platforms.