Barcodes and barcode sets

Torrent Suite™ Software supports sequencing runs in which multiple samples can be processed, or multiplexed. A DNA barcode adapter molecule is used to tag a sample library when it is prepared. The sample is then identified and tracked based on the barcode.

Barcode adapter sets are used to associate multiple adapter barcodes with each individual sample when Planned Runs are set up, or when manual runs of Torrent Suite™ Software plugins are configured. For more information, see Plan step in the workflow bar and Run a plugin manually from the sequencing run report.

During a sequencing run that uses barcodes, Torrent Suite™ Software generates output files with reads that are associated with the barcodes. The barcoded reads are aligned against the reference genome, and results are stored in BAM and BAM index (BAI) files for each barcode. Reads that cannot be classified as into one of the barcodes in the designated set are grouped into a no-match group; alignment against the reference is also performed on the no-match group.

Alignment metrics for each barcoded read are available in the run reports for completed sequencing runs. For more information, see Output files.

A sequencing run on the Ion PGM™, Ion Proton™, Ion S5™, and Ion GeneStudio™ S5 Systems that uses barcodes requires a sample preparation kit that includes a barcode set or kit, such as the Ion Xpress™ barcode set or Ion Torrent™ Dual Barcode Kit 1–96. Torrent Suite™ Software includes barcode sets for the latest available barcode kits.

You can create custom sets of barcode adapters with comma-separated value (CSV) files, then upload these files onto the Ion Torrent™ Server as barcode sets for use during sequencing runs. To create the custom barcode set, you can download a sample DNA barcode set CSV file or an existing DNA barcode set CSV file, customize the DNA barcode set in the file, and import the custom DNA barcode set to the Ion Torrent™ Server.

You can also transfer DNA barcode sets between two different Ion Torrent™ Servers.