The beginning steps of the Torrent Suite™ Software analysis pipeline are shown below:

Steps:

1. The sequencing instrument generates DAT files of electrical signals' raw traces.

2. The signal processing step converts the raw traces into a single number per flow per well, in the 1.wells file.

3. The BaseCaller converts the 1.wells file information into a sequence of bases and writes the sequence into an unaligned BAM file.

4. The BAM file is passed to TMAP for alignment.

The signal processing step also marks several types of low-quality reads:

• Polyclonal reads (reads with two template beads instead of one)

• Reads with high signal processing residual (indicating an ambiguous signal value)

• Reads that do not contain a valid library key

Thesignal processing step marks these problematic reads but does not remove them.