> For the complete documentation index, see [llms.txt](https://help.connected.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.connected.illumina.com/basespace/sequence.md).

# Sequence

- [Sample Sheets](https://help.connected.illumina.com/basespace/sequence/sample-sheets.md)
- [Mapping Sequencing Runs to Biosamples](https://help.connected.illumina.com/basespace/sequence/sample-sheets/ss-mapping-runs-to-bs.md)
- [Fix Indexes](https://help.connected.illumina.com/basespace/sequence/fix-indexes.md)
- [Plan Runs](https://help.connected.illumina.com/basespace/sequence/plan-runs.md)
- [Plan a NextSeq 1000/2000 Run](https://help.connected.illumina.com/basespace/sequence/plan-runs/set-up-planned-run.md)
- [Set up NextSeq 1000/2000 Secondary Analysis](https://help.connected.illumina.com/basespace/sequence/plan-runs/set-up-planned-run/plan-analysis.md)
- [Custom Noise Baseline File](https://help.connected.illumina.com/basespace/sequence/plan-runs/set-up-planned-run/custom-noise-baseline-file.md)
- [Plan a NovaSeq X Series Run](https://help.connected.illumina.com/basespace/sequence/plan-runs/multi-analysis-planned-run.md)
- [Set up NovaSeq X Series Secondary Analysis](https://help.connected.illumina.com/basespace/sequence/plan-runs/multi-analysis-planned-run/novaseqx-plan-analysis.md)
- [NovaSeq X Series Custom Reference File](https://help.connected.illumina.com/basespace/sequence/plan-runs/multi-analysis-planned-run/reference-files.md)
- [Plan a MiSeq i100 Run](https://help.connected.illumina.com/basespace/sequence/plan-runs/miseqi100-planned-run.md)
- [Plan a Run via the API](https://help.connected.illumina.com/basespace/sequence/plan-runs/run-planning-api.md)
- [Create a Custom Index Adapter Kit](https://help.connected.illumina.com/basespace/sequence/plan-runs/custom-index-adapter-kit.md)
- [Import samples](https://help.connected.illumina.com/basespace/sequence/plan-runs/import-samples.md)
- [Requeue a Planned Run](https://help.connected.illumina.com/basespace/sequence/plan-runs/requeue-planned-run.md)
- [Analysis Configuration Template](https://help.connected.illumina.com/basespace/sequence/plan-runs/analysis-configuration-template.md)
- [Prep Tab](https://help.connected.illumina.com/basespace/sequence/plan-runs/prep-tab.md)
- [Create Biological Samples](https://help.connected.illumina.com/basespace/sequence/plan-runs/prep-tab/create-biosamples-prep-tab.md)
- [Import Biological Samples](https://help.connected.illumina.com/basespace/sequence/plan-runs/prep-tab/import-biosamples-prep-tab.md)
- [Prep Libraries](https://help.connected.illumina.com/basespace/sequence/plan-runs/prep-tab/prep-libraries-prep-tab.md)
- [Import Sample Libraries](https://help.connected.illumina.com/basespace/sequence/plan-runs/prep-tab/import-sample-libraries.md)
- [Set Up a Custom Library Prep Kit](https://help.connected.illumina.com/basespace/sequence/plan-runs/prep-tab/create-custom-prep-kit.md)
- [Pool Libraries](https://help.connected.illumina.com/basespace/sequence/plan-runs/prep-tab/pool-libraries-prep-tab.md)
- [Plan Run Using Prep Tab](https://help.connected.illumina.com/basespace/sequence/plan-runs/prep-tab/plan-run-prep-tab.md)
- [Neo Prep](https://help.connected.illumina.com/basespace/sequence/plan-runs/prep-tab/neo-prep.md)
- [Configure](https://help.connected.illumina.com/basespace/sequence/plan-runs/prep-tab/neo-prep/configure-neo-prep.md)
- [Assign Wells](https://help.connected.illumina.com/basespace/sequence/plan-runs/prep-tab/neo-prep/assign-wells-neo-prep.md)
- [Review](https://help.connected.illumina.com/basespace/sequence/plan-runs/prep-tab/neo-prep/review-neo-prep.md)


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