Maximum Seed Length

The --ht-max-ext-seed-len option limits the length of extended seeds populated into the hash table. Primary seeds (length specified by --ht-seed-len) that match many reference positions can be extended to achieve more unique matching, which may be required to map seeds within the maximum hit frequency (--ht-max-seed-freq).

Given a primary seed length k, the maximum seed length can be configured between k and k+128. The default is the upper bound, k+128.