Thermo Scientific appliedbiosystems SeqStudio Flex Series User Manual page 340

Chapter 12 Run calibrations and install checks
12
Perform an install run
Pass/fail criteria for the sequencing install run
Summary tab—sequencing install run
Table 11 Summary tab—sequencing install run
Result
Install run
Install run status
Install run passing criteria
Per-capillary passing
criteria QV20 CRL
(contiguous read length)
limit
# Caps passed and
# Caps failed
# CRL mean and # CRL sd The QV20 mean and standard deviation for all capillaries in the injection.
340
Pass or fail.
The number of capillaries that must pass the QV20CRL limit (described below). If
spectral borrowing is enabled, 22 capillaries must pass for 24-capillary instruments
and 7 capillaries must pass for 8-capillary instruments.
The longest uninterrupted segment of basecalls with an average Quality Value (QV)
≥20.
In addition to evaluating the QV of a basecall, the software considers the QV of
adjacent basecalls within a 21-bp moving window to determine a contiguous read
length based on quality values: the software starts from the 5' end and calculates the
average QV across a moving window size of 21, sliding 1 bp at a time, to the 3' end.
The resulting longest contiguous segment is determined as the CRL.
For QV20CRL limits, see "QV20 CRL limits—sequencing install run"
The number of capillaries that met or did not meet the QV20CRL limit.
SeqStudio ™ Flex Series Genetic Analyzer with Instrument Software v1.0 User Guide
Description
on page 346.