Prepare for Sequencing

The Illumina Microbial Amplicon Prep is compatible with the iSeq 100 i1 reagents v2, the MiSeq reagent kits v2 and v3, the MiniSeq High Output (HO), and the NextSeq 500/550 or 550Dx HO Flow Cell reagent kit.

Use the sample sheet template file for your sequencing system (available on the Illumina support site), to create the sample sheet for your run.

Set Up Sequencing Run

Follow the Illumina support site documentation specific to your sequencing system, and the following information, to set up your run.

Read lengths of 1x75, 2x75, 2x100, 2x150 may be used depending on your assay design. Read length of 2x150 is recommended for most applications.

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For the iSeq Sequencing System:

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Select or enable Run Analysis, Collaboration, and Storage in the system settings.

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For the MiniSeq Sequencing System:

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Select Run Monitoring and Storage as the Configuration option.

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If you are performing surveillance, set your sequencer to use Local Run Manager. Otherwise, use manual mode.

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For a BaseSpace Sequence Hub app, enable monitoring and storage as needed for your instrument.

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Enter the correct read type, depending on your assay design.

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Enter 10 as the value for Index 1 and Index 2.