Indexing Considerations

The process for base calling index reads differs from base calling during other reads.

Index reads must begin with at least one base other than G in either of the first two cycles. If an Index Read begins with two base calls of G, no signal intensity is generated. Signal must be present in either of the first two cycles to ensure demultiplexing performance.

To increase demultiplexing robustness, select index sequences that provide signal in at least one channel, preferably both channels, for every cycle. Following this guideline avoids index combinations that result in only G bases at any cycle.

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Red channel—A or C

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Green channel—A or T

This base calling process ensures accuracy when analyzing low-plex samples.