SampleSheets.md

Sample sheet specification

dorado can make use of a MinKNOW-compatible sample sheet containing data used to identify a particular classification of read. To apply a sample sheet, provide the path to the appropriate CSV file using the --sample-sheet argument:

$ dorado basecaller dna_r10.4.1_e8.2_400bps_hac@v4.2.0 reads/ \
    --kit-name SQK-16S114-24 \
    --sample-sheet <path_to_sample_sheet_csv> \ 
    > calls.bam

A sample sheet can also be applied to the demux command in the same way:

$ dorado demux calls.bam \
    --output-dir classified_reads
    --kit-name SQK-16S114-24 \
    --sample-sheet <path_to_sample_sheet_csv> 

Note that dorado currently uses the sample sheet only for barcode filtering and aliasing, so a --kit-name argument is required.

In the case of demux, the sample sheet must contain a 1-to-1 mapping of barcode identifiers to flow_cell_id/position_id - i.e. all entries in the barcode column must be unique.

Column headers

A sample sheet may only contain the column names below:

Standard	experiment_id	Required*
	kit	Required
	flow_cell_id	Optional if position_id is set
	position_id	Optional if flow_cell_id is set
	protocol_run_id	Optional
	sample_id	Optional*
	flow_cell_product_code	Optional
Barcoding	alias	Optional*
	type	Optional
	barcode	Optional

* These fields must be a maximum of 40 characters, which must be either alphanumeric (A-Z, a-z, 0-9), _ or -.

At a minimum a sample sheet must contain kit, experiment_id and one of position_id or flow_cell_id. All rows in a sample sheet must contain the same experiment_id.

For a full description of the format of the sample sheet, see the MinKNOW Sample Sheet documentation.

Note that dorado does not currently support dual barcodes.

Barcode filtering

If a sample sheet is present and barcoding is requested, dorado will only attempt to find matches to the barcode identifiers listed in the barcode column (if present).

Barcode aliasing

If a sample sheet contains an alias column, this will be used to replace the barcode identifer for reads matching the flow_cell_id/position_id and experiment_id. This will be reflected in the read group ID @RG ID in the file header, and in the BC and RG tags of the classified reads. Values in the alias column must not be valid barcode identifiers (e.g. barcode## or unclassified).

Note that if both flow_cell_id and position_id are present, both must match the read data for an alias to be applied.