Mapping modules

The mapping alternatives supported by TMAP are listed and described in the following table. The map4 module is the default. Other modules are not run unless specifically called, for instance on the Reanalyze screen.

Click the module name link to see the options supported for that module.

Table 1.
Module	Description
TMAP map1 options	BWA-short reads mapping. Very fast at finding perfect matches. Very slow at finding a set of matches with up to two mismatches.
TMAP map2 options	BWA-long / BWASW reads mapping.
TMAP map3 options	Simplified SSAHA, based on a k-mer lookup table.
TMAP map4 options	Based on the BWA fastmap routine. Searches for the maximum exact matches between the reads and reference.
TMAP mapvsw options	A vectorized implementation of Smith-Waterman. A single mapping strategy that is twice as fast as the other modules. Modified to improve specificity.
mapall	A tool that allows algorithms from the map1, map2, map3, map4, and mapvsw modules to be combined into read processing pipelines. The tool allows the read mapping process to be organized into a sequence of up to 9 stages that are sequentially applied to each read. If the read is successfully mapped at one stage, the further stages are not applied to it. At each stage, one or more algorithms can be applied. All hits found by any mapping algorithm are processed together. The syntax for mapall invocation is: tmap <global options> mapall stage1 <stage 1 spec> [stage2 <stage2_spec> [stage3 ....]]], where stageX_spec takes the form: "<stage parameters> mapping_method1 <mapping_method1_params> [mapping_method2 <mapping_method2_params>...]".

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Mapping modules