Fig. 3

Both the PacBio RS II and ONT MinION successfully sequence through repeats, but the RS II had more variable read lengths. After selecting only those reads that could be clearly identified for each plasmid (described in Fig. 1), there were 46,213, 67,339, 9012, and 11,535 PacBio RS II reads for EGFP, SCA36, C9-423, and C9-774, respectively. Likewise, there were 26,735, 39,059, 8276, and 8720 ONT MinION reads for the same respective plasmids. The PacBio RS II generally had more reads, but read length distributions are much tighter for the ONT MinION across all four plasmids, and more closely resemble expected read lengths. The median read length for each instrument is indicated by dashed lines, and the expected maximum read length is indicated by a solid gray line. Expected maximum read lengths for each plasmid were 6080 (EGFP), 5984 (SCA36), 8813 (C9-423), and 9731 (C9-774). Because these long repeat sequences are unstable in plasmids, however, most bacterial colonies contained fewer than the targeted number of repeats (Additional file 1: Figure S1). Thus we expect the read sizes to vary. The additional PacBio RS II read variability may be related to library preparation