TMAP map2 options
The TMAP map2 module implements BWA-long / BWASW reads mapping.
The map2 module is not the default for TMAP, map4 is the default.
The following options are supported with the TMAP map2 module (all are optional).
|
Option |
Type |
Default |
Description |
|---|---|---|---|
|
Integer |
1,024 |
The maximum number of hits returned by a seed. |
|
|
Float |
5.5 |
The coefficient of length-threshold adjustment. |
|
|
Integer |
6 |
The maximum seeding interval size. |
|
|
Integer |
1 |
The maximum number of top-scoring nodes to keep on each iteration. |
|
|
Integer |
5 |
The number of seeds to trigger reverse alignment. |
|
|
Integer |
false |
Remove duplicates for narrow SA hits. |
|
|
Integer |
10,000 |
The maximum gap size during chaining. |
|
|
Integer |
-1 |
The minimum sequence length to examine. -1 to disable. |
|
|
Integer |
-1 |
The maximum sequence length to examine. -1 to disable |