Stacks simulation results. Stacks simulation results. The stickleback reference genome was digested in silico by SbfI, and 60 bp reads were made from each direction from the 22,774 cut sites at several different sequencing depths with several different error rates. The left panel shows the number of (A) loci, (B) stacks, and (C) SNPs observed in the Stacks output. Loci that Stacks assembled incorrectly are displayed in a dark color, whereas loci containing repetitive sequences are shown in a crosshatch pattern. A comparison of the number of loci present in the dataset (A) vs. the number of stacks reconstructed (B) showed that ustacks collapsed repetitive loci but correctly reconstructed nearly all other loci at low and moderate error rates or at high coverage. The right panel shows the number of reads with a certain number of sequencing errors that were incorporated into correct stacks, incorrect stacks, and unused reads for 20× coverage and error rates of (D) 0.5%, (E) 1%, and (F) 3%. As errors accumulated, Stacks excluded more reads, lowering the overall depth, whereas some reads accumulated enough errors to be incorporated into stacks that appeared to be correctly assembled but, in fact, joined stacks representing loci from which they did not originate (indicated by reads with more errors than allowed by the k-mer matching algorithm, four errors in the simulation). Julian M. Catchen et al. G3 2011;1:171-182 ©2011 by Genetics Society of America