Run Design CSV specification for PacBio¶

The Run Design CSV is a comma-separated file which can be imported into SMRT Link to create a run design. Each line in the CSV represents a sample.

Key	Value Example	Value Spec	INTERNAL
Experiment Name	NoRS_Standard_Edna.1	Can be any ASCII string. Defaults to Run Name.
Experiment Id	325/3250057	Must be a valid experiment ID. Details below.
Experiment Description	20170530_A6_Iguana_VVnC_SampleSheet_TEMPLATE	Can be any ASCII string. Defaults to Run Comments.
Run Name	20170530_A6_Iguana_VVnC_SampleSheet_TEMPLATE	Can be any ASCII string.
System Name	Sequel	Must be either Sequel or Sequel II
Run Comments	ecoliK12_pbi_March2013	Can be any ASCII string.
Is Collection	TRUE	Must be a Boolean value. Boolean details below.
Sample Well	A01	Must be a valid well number. Details below.
Sample Name	SMS_Iguana_A6_3230046_A01_TestCase_SB_BindKit_ChemKitv2_8rxnKit	Can be any ASCII string.
Cell No.	1	Must be an integer from 1 to 8. Details below.	True
Sequencing Mode	CLR	Must be either CLR or CCS.
Generate CCS Data	FALSE	Must be a Boolean value. Boolean details below. Default is False.
Movie Time per SMRT Cell (hours)	5	Must be a float >= 0.1 and <= 20 for Sequel, <= 30 for Sequel II
Use Predictive Loading	TRUE	Must be a Boolean value. Boolean details below.
Loading Target (P1 + P2)	0.4	Must be a float between 0.01 and 1.
Maximum Loading Time (hours)	1.2	Must be a float between 1 and 2.
Sample Comment	SMS_Iguana_A6_3230046_A01_TestCase_SB_BindKit_ChemKit	Can be any ASCII string.
Insert Size (bp)	2000	Must be an integer >= 10. Units are in bp.
On-Plate Loading Concentration (pM)	5	Must be a float. Units are in pM.
Size Selection	FALSE	Must be a Boolean value. Boolean details below. Default is False.
Stage Start	FALSE	Must be a Boolean value. Boolean details below. Default is False.	True
Reuse Sample	FALSE	Must be a Boolean value. Boolean details below. Default is False.	True
Template Prep Kit Box Barcode	DM1117100259100111716	Must be valid kit barcode. Details below.
DNA Control Complex Box Barcode	DM1234101084300123120	Must be valid kit barcode. Details below.
Binding Kit Box Barcode	DM1117100862200111716	Must be valid kit barcode. Details below.
Sequencing Kit Box Barcode	DM0001100861800123120	Must be valid kit barcode. Details below.
Wash Kit Box Barcode	DM2222100866100123120	Must be valid kit barcode. Details below.
Automation Name	Diffusion	Can be “diffusion”, “magbead”, or a custom script. Details below.
Automation Parameters	ExtensionTime=double:60\|ExtendFirst=boolean:True	Must follow format demonstrated in Value Example. Details below.
Primary Analysis	Default	Can be any ASCII string.	True
Primary Analysis Parameters	CopyFileTrace=boolean:true	Must follow format demonstrated in Value Example. Details below.	True
Sample is Barcoded	TRUE	Must be a Boolean value. Details on booleans below.
Barcode Set	dad4949d-f637-0979-b5d1-9777eff62008	Must be a uuid for a barcodeset present in the database.
Same Barcodes on Both Ends of Sequence	TRUE	Must be a Boolean value. Details on booleans below.
Barcode Name	lbc1–lbc1	Must be a valid barcode pair.
Bio Sample Name	sample1	Can be any ASCII string.
Pipeline Id	pbsmrtpipe.pipelines.sa3_ds_isoseq3_with_genome	Must be a valid pbsmrtpipe pileine Id
Analysis Name	sample1 analysis	Can be any ASCII string.
Entry Points	PacBio.DataSet.BarcodeSet;eid_barcode;afe89e3f-17ca-e9b8-eae9-b701dbb1f02d	A “\|” separated list with entries: file_type;entry_id;uuid
Task Options	isocollapse.task_options.allow_extra_5exon;boolean;false	A “\|” separated list with entries: task_id;value_type;value

General Requirements¶

The csv may only contain ASCII characters. Specifically, it must satisfy the regular expression:

/^[\x00-\x7F]*$/g

Required Fields¶

Run Name

Sample Well

Sample Name

Movie Time per SMRT Cell (hours)

Insert Size (bp)

Template Prep Kit Box Barcode

Binding Kit Box Barcode

Sequencing Kit Box Barcode

Is Collection¶

This field indicates whether the line is specifying a collection (TRUE), or a barcoded sample (FALSE). Collection lines should leave Barcode Names and Bio Sample Names blank. Barcoded sample lines only need to contain the Is Collection, Sample Name, the Barcode Name, and Bio Sample Name fields.

Experiment ID¶

Experiment IDs cannot contain the following characters: <, >, :, ", \, |, ?, *, or ). Experiment IDs cannot start or end with a “/” and cannot have two adjacent “/”, i.e. “//”. Experiment IDs also cannot contain spaces. Specifically, Experiment IDs cannot satisfy the regular expressions:

/[<>:"\\|?\*]/g

/(?:^\/)|\/\/|(?:\/$)/

/ /g

Cell No.¶

The cell numbers must satisfy a valid cell re-use scheme.

Sample Well¶

The well number must start with a letter “A” through “H”, and end in a number “01” through “12”, i.e. “A01” through “H12”. In other words, it must satisfy the regular expression:

/^[A-H](?:0[1-9]|1[0-2])$/

Automation Name¶

The automation name can be either “diffusion” or “magbead” and is not case-sensitive. A path can also be used, such as “/path/to/my/script/my_script.py”. The path will not be processed further, so if the full URI is required, it must be provided in the CSV, e.g. “chemistry://path/to/my/script/my_script.py”.

Boolean Values¶

Acceptable boolean values for true are:

“true”

“t”

“yes”

“y”

Acceptable boolean values for false are:

“false”

“f”

“no”

“n”

Boolean values are not case-sensitive.

Kit Barcodes¶

The kit barcodes are composed of three parts:

Lot Number (ex: “DM1234”)

Part Number (ex: “100-619-300”)

Expiration Date (ex: “2020-12-31”)

which is used to make a single string. Using the above example, the barcode would be:

DM1234100619300123120

Each kit must have a valid Part Number and cannot be obsolete. The list of kits can be found through a services endpoint such as:

[server name]:[services port number]/smrt-link/bundles/chemistry-pb/active/files/definitions%2FPacBioAutomationConstraints.xml

This services endpoint will list, for each kit, the part numbers (“PartNumber”) and whether it is obsolete (“IsObsolete”). Dates must also be valid, meaning they must exist on the Gregorian calendar.

Parameters¶

The parameters are a “|” separated list. Each item follows the format: [parameter name]=[parameter type]:[parameter value]. Primary analysis parameters are:

Readout

MetricsVerbosity

CopyFileTrace

CopyFileBaz

CopyFileDarkFrame

CopyStatsH5

Acceptable parameter types are:

String

Int32

UInt32

Double

Single

Boolean

DateTime

The parameter names and types are not case-sensitive.

Barcoded Sample Names¶

The barcoded sample names are a “|” separated list. Each item in the list follows the format: [barcode name];[biosample name] The barcode names must be contained within the specified barcodeset. A given barcode name cannont appear more than once in the list. The biosample names can be any ASCII string but cannot contain the field separators “|” and “;”. The biosample names cannot be longer than 40 characters. A maximum of 384 barcodes is permitted per sample.

Auto Analysis fields¶

Auto Analysis is only supported on Sequel II. These fields include: Pipeline Id, Analysis Name, Entry Points, Task Options. You may define one analysis for each collection and bio sample. Pipeline Id, Analysis Name and Entry Points fields are required. The Task Options fields may be left empty, any task options not specified will use pipeline defaults.