As the result of a bug in Kchooser, values of Fraction of Core kmers (FCK) were under-calculated by about a factor of two. As a result, the following sections of the paper were affected. The authors have uploaded a bug-fix version of Kchooser to SourceForge (https://sourceforge.net/projects/ksnp), along with an explanation of the issue.
In the Results and Discussion section, under the “Kchooser, a program to select an optimal k” subsection, there is an error in the third to final sentence and the second to final sentence. In the third to final sentence, “≥0.1” should read “>0.2.” In the second to final sentence, “-0.14029–0.19177log(Branch length), R = 0.99246” should read “-0.24507–0.34278 log(Branch length), R = 0.99265.” The correct sentences are as follow: “Based on these simulations it seems likely that when the fraction of core kmers is >0.2 over 90% of the SNPs will be identified by kSNP. At the optimum k = 13, the fraction of core kmers decreases very regularly as branch length (sequence variation) increases: Fraction of core kmers = -0.24507–0.34278 log(Branch length), R = 0.99265.”
Also in the Results and Discussion section, under the “Consequences of choosing a larger than optimal value of k” subsection, there is an error in the first and third sentences. The number 0.1 should read 0.2. The correct first sentence is as follows: “Table 1 shows that for all of the viral genomes, and for the Acinetobacter genomes, at the optimum value of k the fraction of core kmers is well below 0.2, suggesting that a substantial fraction of the SNPs have not been detected.” The correct third sentence is as follows: “When the fraction of core kmers is below 0.2, there is a risk of missing a significant fraction of the SNPs.”
Citation: The PLOS ONE Staff (2015) Correction: When Whole-Genome Alignments Just Won’t Work: kSNP v2 Software for Alignment-Free SNP Discovery and Phylogenetics of Hundreds of Microbial Genomes. PLoS ONE 10(3): e0118258. https://doi.org/10.1371/journal.pone.0118258
Published: March 3, 2015
Copyright: © 2015 The PLOS ONE Staff. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited