# Prep Libraries

{% hint style="warning" %}
The Prep tab is deprecated and no longer available. For run planning and sequencer integration, see the [Run Planning](/sequence/plan-runs.md) section.
{% endhint %}

## Prep Libraries

{% hint style="warning" %}
If your kit is not listed but is compatible with your sequencing system, set up a custom library prep kit or select a kit that uses the same index adapter set. For example, select Nextera Rapid Capture for TruSight Cardio.
{% endhint %}

1. In the Libraries page, select the Library Prep Kit drop-down arrow, and select a kit.
2. In the Plate ID field, enter a unique plate ID.
3. \[Optional] In the Notes field, enter any notes. For Nextera Rapid Capture libraries, specify that the plate contains multiple enrichments.
4. \[Optional] Assign the sample to a different project.
   1. Select the checkbox of each library to assign to a project.
   2. Select Set Project.
   3. In the Select Project dialog, select or create a project to assign libraries to, and then select Select.
5. Select Auto Prep to automatically assign each library to a well and index location. For Nextera Rapid Capture libraries, samples belonging to the same enrichment must be in the same row. Each plate has a maximum layout of 12 indexes by 8 indexes. If you require more wells or indexes, create multiple plates.
6. \[Optional] To change indexes, select an index on the plate and select a new index from the drop-down list. NOTE: This option is not available for fixed layout plates.
7. \[Optional] Move libraries to a different well as follows. Select the checkbox of the library to move. Drag the selected library from the Libraries area to the appropriate well.
8. Select Export to save your library prep settings in a .csv file. This file serves as a reference when preparing samples in the lab.
9. \[Optional] Select additional plates as follows.
   1. SelectSave and Continue Later to return to Libraries.
   2. Select the checkbox of each library you want to use.
10. Select Pool Libraries.

{% hint style="info" %}
Biological samples are assigned an index even if you are not performing indexed sequencing. During run setup, you can specify no indexing.
{% endhint %}


---

# Agent Instructions: Querying This Documentation

If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question.

Perform an HTTP GET request on the current page URL with the `ask` query parameter:

```
GET https://help.basespace.illumina.com/sequence/plan-runs/prep-tab/prep-libraries-prep-tab.md?ask=<question>
```

The question should be specific, self-contained, and written in natural language.
The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.