Index sets used by the four modes of BFAST for 50 base pair reads from the human genome.

The masks sets for each of the four BFAST modes: accurate, moderate accuracy, moderate speed, and fast are listed under the columns 1, 2, 3, and 4 respectively optimized for 50 base pair reads from the human genome. We prefer to use the accurate setting when aligning to the human genome. The masks used in the main indexes are listed as M, and the masks used in the secondary indexes are listed as S. The key-sizes and key-widths are indicated next to each mask.