Torrent Browser User Interface Guide
Torrent Suite Software space on Ion Community
TMAP map4 Options
This page describes the parameters for the TMAP
map4
module. The
map
4
module is b
ased on the BWA fastmap routine and searches for the maximum exact matches between the reads and reference.
Options supported with the TMAP
map
4
module(all are optional):
| Option | Type | Default | Description |
|---|---|---|---|
| --context | -- | off | Modifies the gap penalty in homopolymers to achieve more accurate alignments |
| --do-repeat-clip | -- | off | Clips repetitive sequence ends of aligned reads |
| --hit-frac | FLOAT | 0.2 | The fraction of seed positions that are under the maximum |
| --end-repair | INT | 0 | Rescues false negatives by selectively forcing alignment at the 3' end of the read. The recommended value is 15. |
| --J | INT | off 2147483647 | Rescues false negatives by selectively forcing alignment at the 3' end of the read. The recommended value is 25. |
| --seed-step | INT | 8 | Thenumber of bases to increase the seed for each seed increase iteration (-1 to disable) |
| --min-seed-length | INT | -1 | Theminimum seed length to accept hits (-1 to disable) |
| --max-seed-length | INT | 48 | Themaximum seed length to accept hits |
| --max-seed-length-adj-coef (-1 to disable) | FLOAT | 2.0 | maximum seed length adjustment coefficient (-1 to disable) |
| --max-iwidth | INT | 20 | Themaximum interval size to accept a hit |
| --max-repr | INT | 3 | The maximumrepresentativehits for repetitive hits |
| --rand-repr | INT | false | Choose the representative hits randomly. Otherwise uniformly |
| --use-min | Boolean | false | When seed stepping, try seeding when at least the minimum seed length is present. Otherwise, use the maximum seed length. |
| --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) |
Torrent Browser User Interface Guide
The Login Page
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BaseCaller Parameters
TMAP Parameters
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