Table 1.
Information about four different viruses used in this study.
Table 2.
Summary of data generated for each of the four viral genomes.
Figure 1.
Histogram plot of the percentage of reads aligned (averaged over 10 runs) for each viral genome.
Histogram plot of the percentage of reads aligned (averaged over 10 runs) for each viral genome shown in Table 2 and each aligner. Reads crossing splice junction regions are shown in pink, reads not crossing splice junction regions are shown in blue.
Figure 2.
Histogram plot of the average alignment accuracy (averaged over 10 runs) for each viral genome.
Histogram plot of the average alignment accuracy averaged over 10 runs for each viral genome shown in Table 1 and each aligner. Reads crossing splice junction regions are shown in pink, reads not crossing splice junction regions are shown in blue).
Table 3.
Summary of S1 and S2 scores for viral reference sequences.
Figure 3.
Histogram plot of the number of aligned reads as a function of the viral mutation rate.
Histogram plot of the number of aligned reads as a function of the mutation rate for each aligner averaged over the four viral genomes (see Table 1).
Figure 4.
Histogram plot of the average accuracy as a function of the viral mutation rate.
Histogram plot of the average accuracy as a function of the mutation rate for each aligner averaged over the four viral genomes (see Table 1).
Table 4.
Summary of values for the measure.
Table 5.
Genome Coverage.
Table 6.
Summary table for reads simulated from the human reference genome.
Table 7.
Summary of S1 and S2 scores for the human reference genome.
Table 8.
Precision, sensitivity and the score for reads simulated from the human reference sequence.
Table 9.
Human reads simulated from host genomic regions not represented in the human (hg19) reference genome.
Table 10.
Runtime measurements.
Table 11.
Alignment results across the HPV16 and the E6/E7 gene regions.
Figure 5.
Coverage plot of the HPV16 E6/E7 gene regions.
The coverage plot of HPV16 E6/E7 gene regions (NC_001526.2) for each aligner using RNA-Seq data sequenced from the transfected (HPV16-E6/E7) human pancreatic duct epithelial cells.
Table 12.
Alignment results across the HBV and its gene regions.