Samples Section
For each run, identify samples to be sequenced in the samples table. The samples table includes the sample ID (The Sample ID field has a 40 character limit), an optional sample name, an optional description, and the indexes used with each sample.
The index columns provide a drop-down list of compatible index sequences based on the Library Kit and Index Kit specified for the run. For runs using custom index sequences, you can enter the sequence as free text.
If the Illumina Proactive monitoring service is enabled, use a sample ID that does not directly identify the patient (e.g. the patient identifier). For information on the benefits of the Proactive Monitoring see Illumina Proactive Techical Note (document # 1000000052503).
When using a custom kit, you must always enter your i5 indexes in forward orientation. Local Run Manager will automatically reverse complement the i5 indexes when writing the sample sheet used for analysis in the iSeq™ 100, MiniSeq™, and NextSeq 500/550™. Local Run Manager will not reverse complement i5 indexes in the MiSeq™.
For analysis modules that require a manifest, the samples table includes a drop-down list of available manifests associated with the module. You can upload and associate a manifest for an analysis module using the Modules & Manifests menu. See Add Manifest Files to an Analysis Module. To import a manifest for a specific run, use the Import Manifests command.
For analysis modules that perform alignment or other methods that require a reference genome, the samples table includes a drop-down list of available genome folders. See Set up a Custom Reference Genome.
You can import samples from a compatible text file and export samples from the samples table for use with another run.
Since sample sheet information can vary on a module-to-module basis, see the workflow user guide for the analysis module you are using for module-specific sample sheet settings.
