Sentence examples for the true alignment from inspiring English sources
Suppose the "true" alignment aligns only the first three symbols (i.e., AAA) of x and y, hence the last three symbols in the respective sequences are regarded as insertions that do not have any matching counterpart in the other sequence.
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.
The sum-of-pairs score (SPS) is the proportion of aligned pairs of nucleotides/amino-acids from the true alignment that are also aligned together in the test alignment.
However, it is still possible to evaluate the relative accuracy by comparing the results from two aligners using the principle that the true alignment tends to have a considerably higher alignment score, because most errors arise from failing to find a seed.
We consider the read to be aligned correctly if at least one of the nucleotides in the read is aligned to the same one in the genome as given by the true alignment.
For each pairwise LCB in the true alignment, we record a TP LCB prediction when the predicted alignment contains at least one correctly aligned nucleotide pair in that LCB.
The aligned reads and called variants are validated against the true alignments and variants, respectively.
In addition, specificity is ensured by statistically separating the true alignments from spurious matches using phred quality values.
The reconstructed alignments were scored against the true alignments and results for ten replicates were recorded.
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.
For the simulated data, network alignment results are compared with the true alignments.
