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Introduction

This documentation provides information on preparing a run manifest for an AVITI System run. A run manifest is a CSV file that prepares sample or cell information for an Element AVITI™ System run. Run manifests also support the analysis or re-analysis of results after a run completes.

  • Bases2Fastq Software uses a run manifest to convert the bases files into FASTQ files and demultiplex pooled libraries based on index sequences for sequencing runs.
  • Cells2Stats Software uses a run manifest to name wells for cytoprofiling runs.

Instrument Workflow Summary​

The onboard instrument software, AVITI Operating Software (AVITI OS), associates every run with a run manifest. If no manifest is provided, AVITI OS writes a default run manifest, otherwise the a run manifest uploaded during run setup is written the run output location.

When processing raw run data by running assignment software, Bases2Fastq or Cells2Stats, you may either:

  • Use the Run Manifest written by AVITI OS to the run output location
  • Run with an alternative run manifest if a manifest was not input at run time or a manifest requires corrections

Default Run Manifest​

If you do not upload a prepared run manifest during run setup, AVITI OS creates a default run manifest based on the run parameters entered. Depending on the run type, sequencing or cytoprofiling, the format of the created manifest is different.

A default sequencing run manifest does not contain index sequences and assigns all reads to one sample per lane during FASTQ generation. Demultiplexing indexed libraries is not possible with a default run manifest. If sequencing indexed libraries, you must perform one of the following options for demultiplexing:

  • Prepare and upload a run manifest with index sequences to the AVITI System.
  • Create a corrected run manifest with all samples and the associated index sequences to use with Bases2Fastq after sequencing completes.

A default cytoprofiling run manifest sets the well label for each well to be equivalent to the well location - e.g. A1. No cell type will be specified, and onboard primary analysis software will also use a generalized segmentation model to segment cells.

Corrected Run Manifest​

The following cases may require a corrected run manifest:

  • You sequenced indexed libraries with a run manifest that does not include index sequences.
  • During a sequencing run setup, you did not upload a run manifest with indexed samples. Use a corrected run manifest with all samples and their associated index sequences to demultiplex.
  • A Bases2Fastq execution failed or reported incorrect results due to incorrect settings or indexes sequences in the run manifest, requiring reprocessing.
  • You need to rename wells or add metadata to a Cells2Stats execution that was not provided at run time.

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.
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