Torrent Suite Software space on Ion Community

User Interface Guide TOC

TMAP Modules

The Torrent Mapping Alignment Program (TMAP) is a sequence alignment software program optimized specifically for Ion Torrent data. TMAP contains several mapping algorithms, each with its own best application. TMAP's current default is map4 .

When you reanalyze a run, you can optionally change both the TMAP module ( map1 , map2 , map3 , map4 , or mapvsw ) and also change the module's parameters.

Mapping modules

This table lists the mapping alternatives supported by TMAP. The map4 module is the default. (Other modules are not run unless specifically called, for instance on the Reanalyze page.)

Click the module name link to see the options supported for that module. See TMAP Global Options for global parameters.

Find the TMAP command for a specific analysis

See Find the TMAP Command for a Completed Run for steps to open the run report log and search for the TMAP command. (The analysis must be completed before you can find the command.)

TMAP examples

This example is the current default setting. Only the map4 module is used.

             tmap mapall -f /results/referenceLibrary/tmap-f3/hg19/hg19.fasta -r /<server_path>/results/analysis/output/Home/Auto_user_G35-685--R65832-110mM_K2SO4-OT_salts-0630_24057_58335/IonXpress_057_rawlib.bam -v -Y -u --prefix-exclude 5 -o 2 stage1 map4
            

This example is the previous TMAP default. This example uses the modules map1 , map2 , and map3 , in that order. Progressively more reads are mapped by each module.

             tmap mapall f <FASTA_file> -v -Y -u --prefix-exclude 5 stage1 map1 map2 map3
            

Access TMAP Frequently Asked Questions on Ion Community: http://ioncommunity.lifetechnologies.com/docs/DOC-9355 .