Availability of Metrics

Not all metrics are available at the early cycles, since some processes need multiple cycles to provide meaningful data. These processes are listed below:

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Template generation occurs at cycle 4 for HCS, or cycle 5 for SCS v2.8 and v2.9; intensities are extracted once the template is generated.

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The software generates phasing/prephasing estimates after cycle 12. Corrected intensities are generated once phasing and prephasing are calculated. Base calls are generated once corrected intensities are generated.

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The software generates quality scoring after cycle 25.

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Alignment to PhiX occurs at cycle 26 – at which point error rates become available, if a PhiX spike-in is being used.