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. Author manuscript; available in PMC: 2020 Nov 2.
Published in final edited form as: Methods Mol Biol. 2013;971:295–312. doi: 10.1007/978-1-62703-269-8_17

Table 2.

Instrument run monitoring and data evaluation

Platform Quality metrics Software Software function
HiSeq2000 GAIIx Raw Cluster Numbers and %PassFilter Clusters allow the assessment of cluster density and performance HCS/SCS (Instrument Control Software) Instrument Control Software provides a graphical interface which allows user view run status and statistics while running the instrument
Intensity and Phasing/Prephasing values allow assessment of the sequencing chemistry performance RTA (Real-Time Analysis) RTA is a component within the Instrument Control Software that monitors the run’s progress, optimizes run conditions and provides run-time quality statistics
Basecall Quality Scores allow assessment of base call quality cycle by cycles SAV (Sequencing Analysis Viewer) SAV is an application that allows user, in real time, to view run quality metrics generated by RTA from an off-instrument remote location