However, the speed of alignments is largely determined by the error rate of the query sequences.
Mapping of reads from each individual to the reference genome sequence was performed with hash size 15 (hs), 100 maximum hash positions (mhp), an alignment candidate threshold (act) of 20, and a maximum mismatch percentage (mmp) of 5. Banded Smith-Waterman algorithm (bw = 41) was used to increase the speed of alignments.
This necessitated a somewhat different design of each pipeline stage, but we sought to retain the core ideas: short, ungapped, multi-hit alignment for initial screening; gradually increasing alignment complexity through multiple filter stages; and parallelization to increase the base speed of each alignment stage.
To enhance the speed of the alignment step, we use a tiered approach instead by dividing our alignment process into two steps: a fast initial assortment of the reads followed by a complete gapped alignment.
However, in the Cochrane review of published randomized controlled trials (RCTs) by Wang et al. [8], no difference in the speed of tooth alignment could be shown after using one initial aligning arch wire over another.
The authors concluded that there is some evidence to suggest that there is no difference between the speed of tooth alignment or pain experienced by patients when using one initial aligning arch wire over another.
It is shown that the initial estimated variance setting of azimuth angle error can influence the speed of initial alignment significantly.
This approach combines the speed of local alignment using BLAST and the accuracy of global NW algorithms to achieve both high throughput and high accuracy.
Using these quality values also decreases the speed of the alignment [ 9].
I investigated the accuracy and speed of the various alignment methods when the true best template sequence was selected for each candidate sequence (Tables 3 and S3).
Note that the speed of KalignP for alignment alone is comparable to Kalign2.
