Our simulation system does not explicitly model gene duplication, and worse, we do not know the true alignment of repeats in the ancestral genomic material, so it is impossible to quantify the accuracy of glocal aligners using our evaluation scheme.
The estimated scale of the problem aligning a billion reads per day on a moderate computer cluster obviously demands extremely fast alignment algorithms, but more importantly demands high accuracy of the alignments (i.e. obtaining the true alignment of a read, among the many various candidates).
This sends a strong signal to Simon investors that there is a true alignment of interest and that the dividend is safe and growing.
Integrated organization may be indicative, however, of performing a chained performance of successive tap events of various durations rather than a true alignment of separate rhythmic pattern streams into a common pulse structure as required in the tasks performed here [58].
Thus, it is critical to find the true alignments of reads that do not match perfectly to the reference, so that sequencing errors can be filtered out via multiple coverage, and so that real variants will not go undetected due to systematic under-mapping of reads with the variant.
In both cases, the soft-clipped local alignment represents the "true" alignment, but the aligner has no way of knowing the location of the SV breakpoint, and thus will instead force a mismatched global alignment or leave the read unmapped.
We will consider a variant of the posterior decoding, in which alignment columns are annotated by the repeat annotation, and an alignment column gets a gain +1, if the true alignment contains the same column with the same label.
Of course, since the true alignment is not known, the accuracy of a network alignment A cannot be measured using (1), hence we cannot directly use this measure to compare different potential alignments to choose the best one.
Ideally, mapping time is largely spent on the matching and validation of true alignments, but if the seed weight is insufficient, the examination of random hits will dominate the running time.
