Article Title: An evaluation of alternative methods for constructing phylogenies from whole genome sequence data: a case study with Salmonella
Figure Lengend Snippet: Characteristics of sample reads by platform. (A) Average number of reads produced, (B) percent of reads mapped to the reference sample, (C) the number of contigs within the assembly, (D) total number of basepairs assembled; dashed red line represent the bps in the reference, and (E) the N50 of the assembly. Boxes depict the interquartile (IQR) range and whiskers indicate 1.5 IQR; the horizontal black line represents the mean. The IonTorrent platform is abbreviated as IonT. Points represent observed values; points were also offset from one another (‘jittered’) to reduce overlap. See Table 1 for sample sizes per NGS platform.
Article Snippet: Given the impact that conclusions derived from such analyses may have, we have evaluated the robustness of clustering individuals based on WGS data to three key factors: (1) next-generation sequencing (NGS) platform (HiSeq, MiSeq, IonTorrent, 454, and SOLiD), (2) algorithms used to construct a SNP (single nucleotide polymorphism) matrix (reference-based and reference-free), and (3) phylogenetic inference method (FastTreeMP, GARLI, and RAxML).
Techniques: Produced, Next-Generation Sequencing