plosone-phylo
Figure 4
Comparison of the clustering of variants across platforms.The ten most common nucleotide V3 sequences from samples 10–65, 10–69, and 10–73 -obtained with each of the four NGS platforms (454™, Illumina®, PacBio®, and Ion Torrent™)- were aligned against the respective population (sanger) sequence from the respective patient using Clustal X 2.0 [76]. For each patient, every unique variant is identified by the NGS platform used and the number of sequences (frequency) obtained, e.g., 454#1290. For each position only those nucleotides that differ from the population sequence are depicted. Dashes indicated the same nucleotide as the population sequence while gaps introduced to maintain the alignment are indicated by dots. Relative clustering of the data from the NGS platforms was inferred by neighbor-joining, phylogenetic analyses determined using MEGA 5.05 [77] and displayed in a circle with topology only to facilitate their interpretation. Bootstrap resampling (1,000 data sets) of the multiple alignments tested the statistical robustness of the trees, with percentage values above 60% indicated by an asterisk. The size of the circles in the phylogenetic trees correlates with the frequency of the unique sequence determined by each NGS platform (color) in the logarithmic scale. The black box denotes the population (sanger) sequence for each sample.
Figure 4
Comparison of the clustering of variants across platforms.The ten most common nucleotide V3 sequences from samples 10–65, 10–69, and 10–73 -obtained with each of the four NGS platforms (454™, Illumina®, PacBio®, and Ion Torrent™)- were aligned against the respective population (sanger) sequence from the respective patient using Clustal X 2.0 [76]. For each patient, every unique variant is identified by the NGS platform used and the number of sequences (frequency) obtained, e.g., 454#1290. For each position only those nucleotides that differ from the population sequence are depicted. Dashes indicated the same nucleotide as the population sequence while gaps introduced to maintain the alignment are indicated by dots. Relative clustering of the data from the NGS platforms was inferred by neighbor-joining, phylogenetic analyses determined using MEGA 5.05 [77] and displayed in a circle with topology only to facilitate their interpretation. Bootstrap resampling (1,000 data sets) of the multiple alignments tested the statistical robustness of the trees, with percentage values above 60% indicated by an asterisk. The size of the circles in the phylogenetic trees correlates with the frequency of the unique sequence determined by each NGS platform (color) in the logarithmic scale. The black box denotes the population (sanger) sequence for each sample.