illumina MiniSeq User Manual

Figure 31 Phasing and Prephasing
A Read with a base that is phasing
B Read with a base that is prephasing.
RTA2 corrects the effects of phasing and prephasing, which maximizes the data quality at every cycle
throughout the run.
Base Calling
Base calling determines a base (A, C, G, or T) for every cluster of a given tile at a specific cycle. The MiniSeq
System uses 2-channel sequencing, which requires only 2 images to encode the data for 4 DNAbases, 1
from the red channel and 1 from the green channel.
Intensities extracted from an image compared to another image result in 4 distinct populations, each
corresponding to a nucleotide. The base calling process determines to which population each cluster
belongs.
Figure 32 Visualization of Cluster Intensities
Base Red Channel
Green
Channel
Result
A 1 (on) 1 (on) Clusters that show intensity in both the red and green channels.
C 1 (on) 0 (off) Clusters that show intensity in the red channel only.
G 0 (off) 0 (off) Clusters that show no intensity at a known location.
T 0 (off) 1 (on) Clusters that show intensity in the green channel only.
Table 1 Base Calls in 2-Channel Sequencing
Clusters Passing Filter
During the run, RTA2 filters raw data to remove clusters that do not meet the data quality threshold.
Document # 1000000002695 v02 Material # 20014309
For Research Use Only. Not for use in diagnostic procedures.
50
MiniSeq System Guide

illumina MiniSeq Specifications

General

Instrument Type	Benchtop Sequencer
Sequencing Technology	Sequencing by Synthesis (SBS)
Read Length	Up to 2 x 150 bp
Output	Up to 7.5 Gb
Run Time	4 - 24 hours
Data Quality	≥ 80% bases ≥ Q30
Maximum Reads	25 million
Sample Capacity	1
Applications	Targeted Gene Sequencing, Small Genome Sequencing, Amplicon Sequencing, Gene Expression Profiling
Power Requirements	100-240 V, 50-60 Hz
Operating Temperature	19°C to 25°C
Operating Humidity	Non-condensing, 20% to 80% RH