TMAP map3 Options
This page describes the parameters for the TMAP map3 module. The map3 module implements a simplified SSAHA, based on a k-mer lookup table.
Options supported with the TMAP map3 module (all are optional):
|
Option |
Type |
Default |
Description |
|---|---|---|---|
|
--seed-length |
INT |
-1 |
The k-mer length to seed CALs (-1 to disable) |
|
--max-seed-hits |
INT |
20 |
The maximum number of hits returned by a seed |
|
--hit-frac |
FLOAT |
0.2 |
The fraction of seed positions that are under the maximum |
|
--seed-step |
INT |
8 |
The number of bases to increase the seed for each seed increase iteration (-1 to disable) |
|
--hp-diff |
INT |
0 |
The single homopolymer error difference for enumeration |
|
--fwd-search |
Boolean |
false |
Use forward search instead of a reverse search |
|
--skip-seed-frac |
FLOAT |
0.2 |
The fraction of a seed to skip when a lookup succeeds |
|
--min-seq-length |
INT |
-1 |
The minimum sequence length to examine (-1 to disable) |
|
--max-seq-length |
INT |
-1 |
The maximum sequence length to examine (-1 to disable) |