Since most Ion Torrent sequencing errors are insertions and deletions, we developed a version of IsoEM capable of handling insertions and deletions in read alignments.
As expected, most 454-errors were insertions or deletions (indels) in homopolymer tracts.
The decoding errors are deletion, insertion, and substitution errors, which are expressed as some discrete 'noise' when mapped to the high-dimensional SVM supervector space (shown in Figure 2).
454 sequencing platforms produce reads of ∼450 nt; errors are usually insertions and deletions (indels) in homopolymer regions.
Approximately 70% of the errors in LR are insertions [ 24].
It is also apparent that the errors are biased towards insertion-deletions (Table 1).
The intervals are slightly asymmetric (Table 1), which corresponds to earlier observations that insertion errors are more common than deletions (Huse et al., 2007; Quinlan et al., 2008).
The types of errors introduced were insertions, deletions or substitutions in 46, 33 and 21% of the cases, respectively.
From Figure 3(a), it can be seen that larger E-model residual errors are attained for the silence insertion PLC scheme (represented by "G ") followed by the AMR codec-cum-PLC.
The beat detection errors are divided into three classes: substitution, insertion and deletion errors.
