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For a given read, the best stratum consists of the alignment(s) with the fewest mismatches.
For a given read, the best alignment was kept if the second-best alignment had two more mismatches, otherwise the read was discarded as non-unique.
Also, the option "-k1" was elected, i.e. if in the course of the search Bowtie found 2 (or more) possible alignments for a given read, the program selected one of the alignments at random.
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The assumption of a search for overlap between the 3' end of the given read and the 5' ends of the remaining reads was assumed when calculating ps.
For all placements of a read, it is only necessary to recalculate pairwise distances between the given read and the n reference sequences, with the pairwise distances among the reference sequences calculated once at the start of the analysis.
Thus, in terms of the alignment matrix of a given read against the SV region we count the k-mer hits by alignment diagonal (Fig. 5).
In 5% of cases, known SNPs revealed additional genomic locations for a given read beyond the original locations, resulting in a superset of the original results.
This uses a fast Single-Instruction-Multiple-Data Smith-Waterman algorithm to align a given read to the entire genome.
Mapping quality (MQ) is a measure of confidence in a given read alignment, given the information available in the reference genome.
Each thread maps the given read to a unique fragment of the genome.
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CEO of Professional Science Editing for Scientists @ prosciediting.com