TMAP modules

The Torrent Mapping Alignment Program (TMAP) is a sequence alignment software program that is optimized specifically for Ion Torrent™ data.

TMAP generally operates in two phases:

• Initial mapping, when the read sequences are located within the reference genome.

• Alignment refinement, when each particular position of the read is aligned to the corresponding position in the reference.

TMAP can run mapping/alignment cycles iteratively, applying different algorithms and parameters to the reads that were not aligned at earlier iterations. In a typical workflow, just one mapping/alignment iteration is used.

TMAP provides several mapping algorithms by using the map1, map2, map3, map4, and mapvsw modules, each with its own best application. The default algorithm is the map4 module.

The alignment refinement phase includes initial alignment using Smith-Waterman or Needleman-Wunch algorithms, and some optional alignment refinement stages that are designed to compensate for specific systematic biases of the sequencing process. Thus:

• The reads can be realigned for better homopolymer alignment (the --context option).

• The portions with likely phasing errors can be realigned with low indel scores (the --do realign option).

• The long indels at the edges of amplicons can be salvaged (the --end-repair option).

• The tandem repeats can be clipped from the read 3' tail (the --do-repeat-clip option).

• The alignment can be performed in flowspace instead of basespace (the --final-flowspace option). In this case the flow signal obtained from the sequencer is aligned with the estimated flow signal from corresponding zone in the reference genome.

When you reanalyze a run, you can change both the TMAP module and the module parameters. Usually, you do not need to modify the default parameter settings. The default TMAP parameters are tuned for Ion Torrent™ data. Modifying these parameters is for advanced users.