Alignment

Reads from each sample are aligned against references specified in the manifest using a banded Smith-Waterman alignment. The banded Smith-Waterman algorithm performs local sequence alignments to determine similar regions between two sequences. Instead of looking at the total sequence, the Smith-Waterman algorithm compares segments of all possible lengths. This process allows alignment across small amplicon targets, often less than 10 bp.

In addition to creating BAM files during alignment, the workflow produces target hits files that contain raw aligned replicate counts for each transcript. For more information, see Target Hits File Format.