Prepare a 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.

CSV File Format

A CSV run manifest has a plain text format that supports multiple sections and metadata. For more information on the CSV file format, see the CSV file format specifications.

• Valid run manifests are encoded in Unicode transformation format, 8-bit (UTF-8).
• The maximum line length is 2048 characters. The line delimiter is “\n” or “\r\n”.
• Blank lines and lines starting with the number sign (#) are valid but skipped.
• Quotation marks (“ ”) optionally enclose field names that contain commas. The quotation marks prompt the software to include the comma and process the field as one entry.

Start from a Template

1. Download a template.
2. Open the template in Excel or a text editor, such as Notepad.
3. Edit the template as desired: modify headings, modify metadata, and add columns.
4. Save the run manifest as a CSV UTF-8 file in an AVITI OS-accessible location.
   • Use a preferred file name.
   • Do not include spaces in the file name.

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

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, Values
[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, see Recording Index Sequences.
6. Save the run manifest as a CSV UTF-8 file in an AVITI OS-accessible location.
   • Use a preferred file name.
   • Do not include spaces in the file name.