Maximum Seed Length
The --ht-max-ext-seed-len option limits the length of extended seeds populated into the hash table. Primary seeds 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). You can specify the length of primary seeds using --ht-seed-len.
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.
Limit Seed Extension
The --ht-max-ext-seed-len option is recommended for short reads, such as reads less than 50 bp. For short reads, it can be helpful to limit seed extension to the read length minus a small margin, such as 1–4 bp. For example, with 36 bp reads, you could set --ht-max-ext-seed-len to 35. The setting makes sure that the hash table builder does not plan a seed extension longer than the read, which would cause seed extension and mapping to fail at run time for seeds that could have fit within the read with shorter extensions.
Seed extension can be similarly limited for longer reads. For example, by setting --ht-max-ext-seed-len to 99 for 100 bp reads. Limiting seed extension for longer reads does not provide as much utility because seeds are extended conservatively in any event. Even with the default k+128 limit, individual seeds are only extended to the lengths required to fit under the maximum hit frequency (--ht-max-seed-freq) and at most a few bases longer to approach the target hit frequency (‑‑ht‑target-seed-freq), or to avoid taking too many incremental extension steps.
