The Single Clone Antibody Analysis operation is an alternate way to annotate and analyze the variable regions of standard IgG-like molecules. It combines the sequences analyzed into fewer representative sequences and can pull out the dominant chain(s) within your dataset.
The Single Clone Analysis operation is particularly suited for analysing Barcoded Sequences from both "single clones in wells" and "single cells in droplets" experiments. It is also suitable for analyzing datasets from NGS technologies that incorporate UMIs. To learn more about Barcodes and UMIs, see this article: Understanding Single Cell technologies: Barcodes and UMIs. The video below provides an overview of these concepts:
For Barcode and/or UMI analysis, you will first need to run the Collapse UMI Duplicates and Separate Barcodes tool. For more discussion about possible workflows, see the Single Cell Analysis workflows article.
Note: The Barcode and UMI functionality is currently available as an add-on. If your organisation does not have Barcode Separation, UMI Collapse, or Single Clone Analysis pipelines enabled, please contact us to try them out.
- How do I run Single Clone Antibody Analysis?
- Single Clone Antibody Analysis Options
How do I run Single Clone Antibody Analysis?
Select one or more nucleotide sequences or lists in your folder and select Annotation > Single Clone Antibody Analysis:
To run the Single Clone Antibody Analysis operation, select options relevant to your sequence data in the dialog that appears and click Run.
Each selected input sequence list will be analysed independently. The pipeline works by:
- Trimming sequences and then applying filtering steps to reduce total data size (configurable)
- De-novo assembling reads together (optional)
- Identifying and annotating Ig-like Antibody regions (FR/CDR)
- Collapsing sequences with similar V(D)J regions into a single dominant sequence. Heavy and light chains are compared separately.
Alternatively when run on barcoded sequences in combination with the Collapse UMI Duplicates and Separate Barcodes operation, it will identify one or more dominant chains for each barcode instead of for each input list. For an example of a workflow for analysing barcoded data, please refer to the UMI/Barcode and Single Clone Analysis tutorials.
The operation will output a Biologics Annotator Result of dominant annotated chains present in your input sequences. The Single Clone Analysis tutorial also contains further information on how to understand Single Clone Analysis Chain Combination tables.