The alignment stage involves aligning reads produced by the pipeline to a reference genome and extracting metrics from those alignments. By default, Torrent Suite™ Software aligns all reads to the genome, however there may be situations, particularly with large genomes, where the alignment takes longer than you are willing to wait. So for such circumstances the Torrent Suite™ Software also can define on a per-reference basis the maximum number of reads that are aligned from a run.

When the number of reads in a run exceeds a genome-specific maximum, a random sample of reads is taken and results are extrapolated to the full run. By sampling a quickly-aligned subset of reads and extrapolating the values to the full run, the software gives you sufficient information to be able to judge the quality of the sample, library, and sequencing run for quality assessment purposes.

The output of the alignment process is a BAM file. The BAM file includes an alignment of all reads, including the unmapped, with exactly one mapping per read. When a read maps to multiple locations, the mapping with the best mapping score is used. If more than one such mapping exists, a random mapping is used and given a mapping quality of zero.