The Torrent Suite™ Software supports barcoded runs, in which multiple barcoded samples are processed on the ION Chip during an Ion sequencing run. A barcode run typically involves sample-prep with an Ion barcode adapter kit (or compatible kit) such that two or more barcode adapters are present in a run. The user selects the barcode set in the run Planning tab of the Torrent Browser. This barcode set information is used during analysis to separate out reads by barcode, remove the barcode and adapters from the read, and output reads by barcode into separate BAM files. Reads are aligned against the reference genome, and results stored in BAM and BAM index (BAI) files for each barcode. Reads that can not be classified as being one of the barcodes in the designated set are grouped into a "no-match'" group, and alignment against the reference also performed on the no-match group.

Alignment metrics for each barcode are available in the Output Files section of the analysis run report. The run report shows Q20 performance metrics for all barcodes in the run, providing a quick glance at the high-level quality of each barcode. The barcode section in the run report also shows the following metrics for each barcode in the run:

• The number of bases

• The number of bases at Q20 (or better) accuracy

• The number of mapped reads

• The mean read length

• A read length histogram

The Torrent Suite™ Software includes barcode sets for the latest available barcode kits. These barcode sets are selected in the run Planning tab. Advanced users optionally can add additional barcode sets in the References section of the Torrent Browser admin tab, either by uploading a CSV file of all barcodes or by manually adding each barcode.