Smith-Waterman Alignment Scoring Options
Refer to Smith-Waterman Alignment Scoring Settings for more details about the alignment algorithm used within DRAGEN. The following scoring options are specific to the processing of canonical and noncanonical motifs within introns.
| • | --Aligner.intron-motif12-pen |
The --Aligner.intron-motif12-pen option controls the penalty for canonical motifs 1/2 (GT/AG, CT/AC). The default value calculated by the host software is 1*(match-score + mismatch-pen).
| • | --Aligner.intron-motif34-pen |
The --Aligner.intron-motif34-pen option controls the penalty for canonical motifs 3/4 (GC/AG, CT/GC). The default value calculated by the host software is 3*(match-score + mismatch-pen).
| • | --Aligner.intron-motif56-pen |
The --Aligner.intron-motif56-pen option controls the penalty for canonical motifs 5/6 (AT/AC, GT/AT). The default value calculated by the host software is 4*(match-score + mismatch-pen).
| • | --Aligner.intron-motif0-pen |
The --Aligner.intron-motif0-pen option controls the penalty for noncanonical motifs. The default value calculated by the host software is 6*(match-score + mismatch-pen).