The PGM quality clip was extracted from the SFF file produced from Torrent Server 2.0.1. To emulate the PGM HRI trim approach, we calculated the percentage of HRI 1-mers and 2-mers out of the total 1-mer and 2-mer calls in the read, and continued clipping from the 3′ end until this percentage reached 3% or less (Torrent User Documentation 2.20). Our third HRI trim approach included HRI 3-mers (defined as flow-values in [2.50, 2.59] or [3.40, 3.49] in this calculation. As with the Torrent Server software, reads shorter than 4 bp after clipping were ignored.
