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.

Module	Description
map1	BWA-short reads mapping Very fast at finding perfect matches Very slow at finding a set of matches with up to two mismatches
map2	BWA-long / BWASW reads mapping
map3	Simplified SSAHA, based on a k-mer lookup table
map4	Based on the BWA fastmap routine Searches for the maximum exact matches between the reads and reference
mapvsw	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 command to quickly map short sequences to a reference genome.