Torrent Browser User Interface Guide
Torrent Suite Software space on Ion Community
TMAP map1 Options
This page describes the parameters for the TMAP
map1
module. The
map1
module implements
BWA-short reads mapping and has these characteristics:
-
map1
is very fast at finding perfect matches -
map1
is very slow at finding a set of matches with up to two mismatches
Options supported with the TMAP
map1
module(all are optional):
--seed-length | INT | 32 | The k-mer length to seed CALs (-1 to disable) |
--seed-max-diff | INT | 2 | The maximum number of edits in the seed |
--seed2-length | INT | 48 | The secondary seed length (-1 to disable) |
--max-diff | NUM | 0.04 | The maximum number of edits or false-negative probability assuming the maximum error rate |
--max-error-rate | FLOAT | 0.02 | The assumed per-base maximum error rate |
--max-mismatches | NUM | 3 | The maximum number of or (read length) fraction of mismatches |
--max-gap-opens | NUM | 1 | The maximum number of or (read length) fraction of indel starts |
--max-gap-extensions | NUM | 6 | The maximum number of or (read length) fraction of indel extensions |
--max-cals-deletion | INT | 10 | The maximum number of CALs to extend a deletion |
--indel-ends-bound | INT | 5 | The number of bps from the end of the read |
--max-best-cals | INT | 32 | Optimal CALs have been found |
--max-nodes | INT | 2000000 | The maximum number of alignment nodes |
--min-seq-length | INT | -1 | The minimum sequence length to examine (-1 to disable) |
--max-seq-length | INT | -1 | Themaximum sequence length to examine (-1 to disable) |
Option
|
Type
|
Default
|
Description
|
---|
Torrent Browser User Interface Guide
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