Ion instrument data types

Signal processing input files

Signal processing input files (4 files per cycle) consist of the raw voltage measurement data collected during the sequencing run. On the Ion PGM™ System, you can reanalyze a run with the signal processing input file, which is available on the instrument.

Keep the signal processing input data if you want to reanalyze the run starting from raw signal processing data.

However, on the Ion Proton™ or Ion S5™ Systems, signal processing input data are used on the instrument, then deleted. These files are available on Torrent Suite™ Software only as thumbnails for the Ion Proton™, Ion S5™ Systems, or Ion GeneStudio™ S5 Systems.

Basecalling input files

Signal processing input files are converted to a single condensed basecalling input file representing the processed signal.

Keep or archive basecalling input data if you want to reanalyze the run. This can save time and resources because reanalyses use the basecalling input data, rather than the raw signal processing input data.

On the Ion Proton™, Ion S5™ Systems and Ion GeneStudio™ S5 Systems, basecalling input data are transferred to the Ion Torrent™ Server and are available for reanalyses.

Output files

Output files consist of all BAM files, run reports, and plugin results.

It is important to keep and archive these files. Delete output files only if you are sure that you no longer need the files.

Intermediate files

Intermediate files contain information used for debugging runs.

You can delete these files immediately after instrument runs, without affecting data.