TMAP map3 options
The TMAP map3 module implements a simplified SSAHA, based on a k-mer lookup table.
The map3 module is not the default for TMAP, map4 is the default.
The following options are supported with the TMAP map3 module (all are optional).
|
Option |
Type |
Default |
Description |
|---|---|---|---|
|
Integer |
-1 |
The k-mer length to seed CALs. -1 to disable |
|
|
Integer |
20 |
The maximum number of hits returned by a seed. |
|
|
Float |
0.2 |
The fraction of seed positions that are under the maximum. |
|
|
Integer |
8 |
The number of bases to increase the seed for each seed increase iteration. -1 to disable |
|
|
Integer |
0 |
The single homopolymer error difference for enumeration. |
|
|
Boolean |
False |
Use forward search instead of a reverse search. |
|
|
Float |
0.2 |
The fraction of a seed to skip when a lookup succeeds. |
|
|
Integer |
-1 |
The minimum sequence length to examine. -1 to disable |
|
|
Integer |
-1 |
The maximum sequence length to examine. -1 to disable |