Bcl2fastq2 Sample Sheet Generation (NGS v5.16 and earlier)
Compatibility and Package Version:
| • | Support for bcl2fastq v2.15 sample sheet generation is available in multiple Illumina sequencer integration packages. Refer to the release notes for your installed package for information about the features available. |
| • | Support for single and dual indexes, and indexes of different lengths, on a single flow cell has been validated and is supported with HCS v3.3.76 |
This article discusses the Illumina sequencer integration packages that generate a sample sheet for use with bcl2fastq v2.15 analysis software.
Sample sheet generation is configured on the step prior to the sequencing run, which is the step where samples are placed on the flow cells or reagent cartridges that will be placed in the instrument.
The sample sheet is generated by means of a script, which the user initiates by clicking a button on the Record Details screen of the step. This generates a bcl2fastq2 format sample sheet file for the container loaded during the step, where the name of the sample sheet will be <container name>.csv.
|
Field Name |
Field Type |
Notes |
|
Experiment Name |
Text |
|
|
Workflow |
Text |
|
|
Read 1 Cycles |
Numeric |
|
|
Read 2 Cycles |
Numeric |
Entering a value other than 0 indicates a paired-end reads run |
|
Adapter |
Text |
Required if using 'Adapter Read 2' |
|
Adapter Read 2 |
Text |
|
|
Mask Adapter |
Text |
Required if using 'Mask Adapter Read 2' |
|
Mask Adapter Read 2 |
Text |
|
Field Name |
Field Type |
Required? |
Notes |
|
Description |
Text |
No |
The following table lists the parameters used by the script.
|
Parameter |
Description |
||||||
|
u, username |
LIMS username (Required) |
||||||
|
p, password |
LIMS password (Required) |
||||||
|
i, processURI |
LIMS process URI (Required) (lowercase I) |
||||||
|
c, csvFileLimsIds |
Sample sheet CSV file LIMS ID (Required - may be provided multiple times) |
||||||
|
e, errorLogFileName |
Log file name (Required) |
||||||
|
l, useProjectLimsID |
Project LIMS ID will be used instead of project name in the Project column of the sample sheet (Optional)
|
||||||
|
s, useSampleLimsID |
Sample LIMS ID will be used instead of sample name in the SampleName column of the sample sheet (Optional) (S ee Enabling unique FASTQ file names )
|
||||||
|
a, appendLimsID |
LIMS ID of the protocol step will be appended to sample names in the SampleName column of the sample sheet. (Optional) Use this option to guarantee unique FASTQ file names per run. (See Enabling unique FASTQ file names)
|
||||||
|
-r, useReverseComplement |
If paired-end reads are used, the reverse complement of index2 will be displayed instead of the standard sequence.
|
Usage
Below is an example automation command showing the script in use. The sample sheet generation portion of the parameter string is shown in bold.
bash -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/<package_name>/<package_version>/EPP/<extensions.jar> \
-u {username} \
-p {password} \
-i {processURI:v2} \>
script:generate_bcl2fastq_sample_sheet \>
-c {compoundOutputFileLuid3} \>
-e {compoundOutputFileLuid4}"
All one-dimensional container types with both numeric rows and numeric columns are supported.
The following table lists the fields that are always populated in the sample sheet, along with all other fields that may also be present.
Note the following:
| • | In the table, only items in bold are used by the bcl2fastq2 tool when processing. Other fields will be ignored by the tool and are included for your convenience. |
| • | If no upstream pooling is detected, BaseSpace Clarity LIMS will populate the sample sheet with the SampleID and SampleName of the submitted sample; other fields are populated with data from the samples that were input to the step (i.e. derived samples). |
| • | If upstream pooling is detected, BaseSpace Clarity LIMS will populate the sample sheet with the first upstream pooled inputs found – not with the submitted sample or step input fields. |
For information about ordering of sample sheet data, illegal characters, and other rules and constraints, see Rules and constraints .
|
Field Name |
Always Present? |
Populated by |
Comments |
|
[Header] |
Static text |
||
|
Investigator Name |
Yes |
LIMS technician name |
|
|
Experiment Name |
No |
Step UDF |
Always present in NextSeq v1.0.1. If the UDF is not entered then the line will display as "Experiment Name". |
|
Date |
Yes |
Script run date |
|
|
Workflow |
Yes |
Step UDF |
|
|
[Reads] |
Static Text |
||
|
Read 1 Cycles |
No |
Step UDF |
|
|
Read 2 Cycles |
No |
Step UDF |
|
|
[Settings] |
Static text |
||
|
Adapter |
No |
Step UDF |
Required if AdapterRead 2 is used. |
|
AdapterRead 2 |
No |
Step UDF |
|
|
MaskAdapter |
No |
Step UDF |
Required if MaskAdapterRead 2 is used. |
|
MaskAdapterRead 2 |
No |
Step UDF |
|
|
[Data] |
Static text |
||
|
Lane |
Yes |
Sample Output Placement |
Not present for NextSeq v1.0.1. |
|
SampleID |
Yes |
Sample LIMS ID |
|
|
SampleName |
Yes |
Sample Name |
Depending on the command-line value, this will either be the sample name or the LIMS ID of the submitted sample of the input. The additional '-a' command line option appends the LIMS ID to the end of this value, e.g."Sample1-1234" (see Script parameters and usage ) |
|
SamplePlate |
Yes |
Sample input plate |
This will be the input plate to the current step. If the input is a pool,then this will be the input plate of the given sample prior to entering the pool. |
|
SampleWell |
Yes |
Sample input well location |
This will be the well location of the sample on the input plate. If the input is a pool, then this will be the well location of the given sample prior to entering the pool. |
|
index |
No |
Sample reagent label |
Dual index reagents will contain a hyphen-separated DNA sequence. This field will use the first half of that value. |
|
index2 |
No |
Sample secondary reagent label |
Dual index reagents will contain a hyphen-separated DNA sequence. This field will use a second half of that value. |
|
Project |
Yes |
Sample project |
Will be the name of LIMS ID of the project for the sample (see Script parameters and usage ) |
|
Description |
Yes |
Submitted sample UDF |
This section outlines the format and contents of the generated sample sheet and associated log file.
When validating the installation of your integration, refer to this information to ensure that the sample sheet and log files are correctly generated.
|
Note: The sample sheet file supports single and dual indexes, and indexes of different lengths, on a single flow cell (currently tested and supported with HCS v. 2.2.70 only). See Information and warning messages . |
Bcl2fastq2 sample sheet
| • | When single and dual indexes are present in the same flow cell: |
No information or warning messages display if indexes of different lengths are present on the same flow cell.
To enable sample sheet generation for multiple containers, you must modify the process type on which the sample sheet generation automation is configured, creating a placeholder for each file:
To enable unique FASTQ file names per sequencing run, the EPP command on the process type must be configured to use the following parameter options:
.
