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Sample sheet

Sample sheets are used in multiple ways inside MinKNOW, either as a way to configure a sequencing run, or as a document of the configuration of the sequencing run.

Output columns

The following fields document fields MinKNOW will write at the end of a sequencing run.

protocol_run_id

Regex [0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}
Required
Examples
e4994c62-93f9-439a-bc8f-d20c95a137a5

A random-generated uuid for the sequencing protocol (eg: e4994c62-93f9-439a-bc8f-d20c95a137a5) This consists only of lower-case ASCII letters (a-z), digits (0-9) and dashes (-).

position_id

Regex [A-Z-0-9]+
Required
Examples
MN12345

The device identifier used for sequencing.

flow_cell_id

Regex [A-Z0-9_-]+
Required
Common fields FASTQ: flow_cell_idBAM: PU
Examples
FXX12345
PXX12345
AAA123

The human-readable identifier for the flow cell (eg: FAK54854).

sample_id

Regex [a-zA-Z0-9_\.-]+
Required
Common fields FASTQ: sample_idBAM: LBSequencing summary: sample_id
Examples
My_Sample
my-sample-1

Set by the user in the GUI as "Sample ID".

experiment_id

Regex [a-zA-Z0-9_\.-]+
Required
Examples
My_Group
my-group-1

Set by the user in the GUI as "Experiment ID".

flow_cell_product_code

Regex [A-Z0-9-]+
Required
Examples
FLO-PRO114
FLO-MIN114

The product code of the flow cell used in the experiment

kit

Regex [A-Z0-9-]+
Required
Examples
SQK-LSK114

The product code of the kit used in the experiment

barcode

Regex barcode([0-9]+)
Required
Only When has_input_sample_sheet
Common fields FASTQ: barcodeBAM: SMSequencing summary: barcode_arrangement
Examples
barcode01

The barcode identified for the read.

alias

Regex [A-Za-z0-9\-_\.]+
Required
Only When has_input_sample_sheet
Common fields FASTQ: barcode_aliasBAM: alSequencing summary: alias
Examples
my_sample
sample01

User-specified identifier used for the barcode, if available, otherwise the arrangement name.

type

Regex na|test_sample|positive_control|negative_control|no_template_control|positive_control_1|positive_control_2
Required
Only When has_input_sample_sheet
Examples
positive_control
no_template_control

The specified type of the barcode, or "na", if not available.

Input columns

When passing a sample sheet into MinKNOW, different rules apply to the columns - not all are required.

Column Notes
flow_cell_id Optional if position_id is specified and the flow cell has flow_cell_id on the EEPROM. Used to identify which position to apply values to.
position_id Optional if flow_cell_id is specified. Used to identify which position to apply values to.
sample_id Optional. An individual position can only have one sample_id assigned to it when starting a run.
experiment_id Each row in the sample sheet must contain an experiment_id.
flow_cell_product_code Required if the product code is not available on the EEPROM. Used to find the correct protocol to start.
kit Required Kit is used to find a protocol to start.

Notes

If position_id and flow_cell_id are both defined, the flow_cell_id will be validated against the EEPROM value. The flow_cell_id will be set against the user_specified_flow_cell_id when starting a protocol.

All rows must contain the same experiment_id value, therefore, the sample sheet will only have a single experiment_id defined overall but the entries on each row are validated.

If expansions kits are additionally defined they should be space separated, e.g., SQK-LSK109 EXP-NBD104 EXP-NBD114 or OND-SQK-LP0096S. The sample sheet must contain exactly one sequencing kit, but can contain 0, 1, or many, expansion kits. The sequencing kit must be specified before any expansion kits.