Prepare a Sequencing Manifest

When preparing a run manifest, start with a template or create and populate an original CSV file. Element recommends at least completing the Settings and Samples sections.

Manifest Sections

A sequencing run manifest file includes the following sections. Each section starts with a bracketed section heading 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 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 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 by library prep workflow. LoopSeq™ for AVITI libraries include Elevate™ indexes and adapters and therefore are considered Elevate libraries.

• 16S LoopSeq for AVITI
• Amplicon LoopSeq for AVITI
• Element Adept™ Library Compatibility Workflow
• Element Elevate Library Prep Workflow
• A third-party workflow with a Cloudbreak Freestyle™ 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: e.g., modify metadata, 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 an AVITI OS-accessible location or upload during planned run creation to validate the manifest before run start.

Template Manifests

Downloadable Template	Contents	AVITI OS Version	Indexing
Adept and Third Party Run Manifest Template	Minimal metadata (uses default settings) PhiX Control Library index sequences Example samples	v2.0.0 and later	Depends on library prep
Adept and Third Party Run Manifest Template with Metadata	Contains all metadata (uses default settings) PhiX Control Library index sequences Example samples	v2.0.0 and later	Depends 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
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 other 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. If necessary, add any of the following optional 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.