Analysis pipeline overview

The following depicts and describes the beginning steps of the Torrent Suite™ Software analysis pipeline.

Steps:

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

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 module 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 the TMAP module 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.

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