This algorithm takes advantage of EST library redundancy and performs four filters to reduce the effect of sequencing inaccuracies at each position.
However, a major drawback to the 454-Roche platform is the susceptibility of over/under and delayed base calling, either of which can lead to sequencing inaccuracies [ 55].
In most cases, those insertions and deletions were only present in 1 out of the 35 strains, and were likely a result of sequencing inaccuracies.
Revisiting and updating existing genome annotations is absolutely essential, as not only does it allow the opportunity to increase the users understanding of the organism in question, but it also improves accuracy for downstream users when performing automated annotations of related species [ 21, 22], reducing the introduction of errors caused by historic sequencing inaccuracies.
In comparison to early studies which reported a sequencing inaccuracy rate of ~13 18% (Quail et al. 2012; Mosher et al. 2013), more recent studies have reported a large reduction in these rates (Schloss et al. 2015).
Note that because the algorithm finds the best alignment between the two sequences, small inaccuracies in the input transcription will not reduce the quality of the final animation.
We noted earlier that the quality of some genome sequences, and inaccuracies in their annotations, were initially obstacles to this study (see supplementary information, Supplementary Material online, for an example).
While per-base error rate in most NGS methodologies is low, technical limitations, insufficient sequencing depth, and sequence and structural inaccuracies in the reference genomes can result in numerous errors [ 9].
In some cases, template sequence discrepancies or inaccuracies can lead to failed assays caused by poor or no binding of primers and probes and/or non-specific binding resulting in multiple PCR products.
Thus, the previously published result is likely due to sequencing or annotation inaccuracies.
