Prepare a sequencing manifest

Prepare a sequencing run manifest from a template or an original CSV file.

When you prepare a run manifest, start with a template, or create and populate an original CSV file. Element Biosciences™ recommends to at least complete the Settings and Samples sections.

Manifest sections

A sequencing run manifest file includes the following sections. Each section starts with a bracketed section heading that is followed by a row of column headings. Section and column headings are case insensitive. All subsequent rows list metadata for the section.

• Samples: Identifies the libraries that are sequenced in a run and any corresponding index sequences.
• Settings: Specifies settings for Bases2Fastq™ processes, such as adapter trimming and base masking for demultiplexing.
• Run Values: Adds custom information to Bases2Fastq output so that you can annotate the metadata.

Library prep workflows

A sequencing run manifest supports the following library prep workflows. Metadata in the Settings and Samples sections can vary based on the library prep workflow.

• Element Adept™ Library Compatibility Workflow
• Element Elevate Library Prep Workflow
• A third-party workflow with a Cloudbreak Freestyle™ sequencing kit
• A third-party workflow with a Trinity™ sequencing kit

For workflow guides, see User Documentation.

Tip:

To get started with a library prep, use a downloadable run manifest template.

Start from a template

1. Download a template.
2. Open the template in Excel or a text editor.
3. Edit the template as desired (for example, modify metadata or add columns).
4. Save the run manifest as a CSV UTF-8 file.
   • Allowed characters in file name are are letters, numbers, dash, dot, parentheses, and underscore.
   • Do not include spaces in the file name.
5. Move the file to a location that AVITI OS can access. Or, upload the file when you create a planned run to validate the manifest before run start.

Template manifests

Downloadable Template	Contents	AVITI OS Version	Indexing
Adept or Third Party Run Manifest Template	Minimal metadata (uses default settings) PhiX Control Library index sequences Example samples	v2.0.0 and later	Based on library prep
Adept or Third Party Run Manifest Template - Full Metadata	Contains all metadata (uses default settings) PhiX Control Library index sequences Example samples	v2.0.0 and later	Based on library prep
Elevate Run Manifest Template	Minimal metadata (uses default settings) PhiX Control Library index sequences Elevate Cloudbreak Index Sequences	v2.0.0 and later	I1: 12 bp I2: 9 bp
Elevate Trinity Run Manifest Template	Minimal metadata (uses default settings) PhiX Control Library index sequences Twist, IDT, or Elevate Library Index Sequences	v2.1.0 and later	I1: 12 bp I2: 9 bp

Create an original file

1. Open a new file in Excel or an application that can save CSV files.

2. Enter any of the following section headings and their column headings:

   [RunValues]
   KeyName,Value
   [Settings]
   SettingName, Value
   [Samples]
   SampleName, Index1, Index2,

3. (Optional) Add the following column headers:

   • Settings: Lane
   • Samples: Lane, Project, ExternalID, or Custom Metadata per Sample

   [Settings]
   SettingName, Value, Lane
   [Samples]
   SampleName, Index1, Index2, Lane, Project, ExternalId, CustomMetadata

4. If necessary, add metadata to the Run Values and Settings sections.

5. For multiplexed libraries, add the Samples section.

   • For detailed guidance on index setup, see Recording Index Sequences.

6. Save the run manifest as a CSV UTF-8 file.

   • Allowed characters in file name are are letters, numbers, dash, dot, parentheses, and underscore.
   • Do not include spaces in the file name.