The base-calling software in the Torrent Suite (version 2.0.1) performs two quality assurance steps prior to outputting sequences. The first step evaluates the residual between observed flow values and predicted flow values, based on a model of the flow cell. Reads with residuals that produce a median absolute value greater than a given threshold are filtered from both the SFF and the FASTQ, as they are assumed polyclonal. The second step scans non-polyclonal reads to identify undesirable 3′ regions of the read, which are subsequently trimmed. Undesirable regions are defined as regions containing the adapter sequence (and beyond) as well as low-quality regions. Should both adapter and quality trims be specified, the more stringent trimming is used. The newly released Torrent Suite (2.20) introduced a third trimming approach which clips the read based on high-residual ionogram (HRI) 1-mer and 2-mer flow values, which may indicate ‘noisy’ flows. A high-residual 1-mer is in the range [0.50, 0.59] or [1.40, 1.49], a high residual 2-mer in the range [1.50, 1.59] or [2.41, 2.49] (Torrent User Documentation Version 2.2.0).
