About references
Torrent Suite™ Software provides access to references for use in your sequencing runs. References are available for reference genome sequences, barcode sets, test fragments, and other files that filter or restrict genomic sequencing and analysis to the regions of interest. Before you can use some of these files in sequencing runs, you must upload or import the files to the Ion Torrent™ Server that is connected to the sequencing instrument.
References are accessed in Torrent Suite™ Software by clicking 
(Settings) > References, and using options in the left navigation menu.
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Reference type |
Description |
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Import preloaded Torrent Suite™ Software validated reference genome sequences, or a custom reference genome to add them to Planned Runs and Planned Run templates. |
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Reference sequences become obsolete and are listed in the Obsolete References Sequences screen after Torrent Suite™ Software is updated with a release that includes a new TMAP index. |
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Upload these files to add them to your Planned Runs. |
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Upload hotspots files to add them to your Planned Runs. The variantCaller plugin generates output files that include these positions whether or not a variant is called, and include evidence for a variant and the filtering thresholds that disqualified a variant candidate. |
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Use these known sequences to monitor system characteristics. |
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Upload Ion barcode sets or your own custom barcodes sets for use in sequencing runs. |
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Review records of recent uploads of target regions, hotspots, and ZIP files from AmpliSeq.com. |