DNA Mapping

DRAGEN primarily maps reads by finding exact reference matches to short seeds. However, DRAGEN can also map seeds differing from the reference by one nucleotide by also looking up single-SNP edited seeds. Seed editing is usually not necessary with longer reads (100 bp+), because longer reads have a high probability of containing at least one exact seed match. Seed editing is also not necessary if using paired ends, because a seed match from either mate can successfully align the pair. However, seed editing can be useful to increase mapping accuracy for short single-ended reads, with some cost in increased mapping time. The following options control seed editing:

Seed Editing Options

Command-Line Option Name

Configuration File Option Name