Run Planning provides a list of Illumina index adapter kits used for sequencing. If your index adapter kit is not available, please follow the following instructions to create a custom one.
Creating a custom index adapter kit can be done from within Run Planning (when creating a Configuration) or from the Resources page (select Index Adapter Kit tab).
A custom Index kit can be configured in yaml or tsv.
The following are basic rules to follow when configuring in yaml
3 dashes indicates the start of the definition
Begin a comment line with '#' character
Each line is typically in the format of SettingName: SettingValue. Setting which value is a string has to be enclosed in double quotes. Other types like numeric or boolean do not require double quotes.
When a setting contains more complex information, it is usually defined in multiple lines. Ensure the right indentation to maintain the structure. Use two space characters instead of a tab character.
Three yaml templates are provided.
Non-fixed Layout: for non-fixed layout kit where any index can be selected for any sample.
Fixed Layout - Single Plate: for fixed layout kit with single plate, where each well has a defined index combination.
Fixed Layout - Multi Plate: for fixed layout kit with multi-plate, where each well has a defined index combination.
| Level-1 Setting | Level-2 Setting | Description |
|---|---|---|
The supported values are "Dual", "Single", and "NoIndex". Create a list below this setting. Each list item should be preceded with a dash (-) character and enclosed in double quotes. Use two spaces for indentation. See Example 1.
i7Index1 Create a list of Index1 sequences below this setting. Each index should be in the format of IndexName: "IndexSequence". See example 2.
i5Index2 Create a list of Index2 sequences below this setting. Each index should be in the format of IndexName: "IndexSequence". See example 2.
The mapping should be defined in the format of "WellPosition/Index1Name-Index2Name" or "Plate-WellPosition/Index1Name-Index2Name". The allowed well positions are A01 - H12. If the kit requires well positions defined in different format, define FixedLayoutPositionKeyByIndexId: true. See example 4, example 5, example 6.
The value is true or false. However, the usage is currently restricted to Instrument Platforms which allow multi-configuration. As each configuration only allows one Override Cycles, when setting up a run, samples with different index lengths should be separated into different configurations.
EnableCustomIndexCycles
The value is true or false. If the setting is set to false or if the setting is not defined, the Override Cycles used is Y;I;I;Y pattern.
NumCyclesIndex1Override The value should be a numeric value. If this setting is not defined, the number of Index1 cycles follows the number of bases in the Index1 sequences.
NumCyclesIndex2Override The value should be a numeric value. If this setting is not defined, the number of Index2 cycles follows the number of bases in the Index2 sequences. See example 7.
OverrideCycles
The value should be defined in this format: "Y{{Read1Length}};I{{Index1Length}};I{{Index2Length}};Y{{Read2Length}}?", where:
{{Read1Length}} is the number of cycles for Read1,
{{Read2Length}} is the number of cycles for Read2,
{{Index1Length}} is the number of cycles for Index1, and
{{Index2Length}} is the number of cycles for Index2.
If UMI is used, update the pattern accordingly.
E.g. if Read1 and Read2 cycles include 7 UMI cycles and 1 skipped-cycle: U7N1Y{{Read1Length-8}};I{{Index1Length}};I{{Index2Length}};U7N1Y{{Read2Length-8}}?"
E.g. if the kit is a single index kit, with UMI cycles instead of Index2: "Y50N{{Read1Length-50}};I8N{{Index1Length-8}};N{{Index2Length-16}}U16;Y50N{{Read2Length-50}}?". See example 7.
This section contains custom BCL Convert settings. The settings will be included in the sample sheet generated by Run Planning.
TrimUMI Indicates if the UMI should be excluded from fastq files. The value is "0" or "1". Set to "0" if BCL Convert should still output UMI cycles to fastq files. See example 8.
CreateFastqForIndexReads Indicates if the UMI in Index cycles should be trimmed or not. The value is "0" or "1". Set to "1" if BCL Convert should still output UMI cycles in Index to fastq files. Note that TrimUMI should also be set to "0".
Similar to yaml, three tsv templates are provided. Please note that currently .tsv file supports fewer custom kit settings (as compared to .yaml file).
Non-fixed Layout: for non-fixed layout kit where any index can be selected for any sample.
Fixed Layout - Single Plate: for fixed layout kit with single plate, where each well has a defined index combination.
Fixed Layout - Multi Plate: for fixed layout kit with multi-plate, where each well has a defined index combination.
A tsv file contains of three sections, namely [IndexKit], [Resources], [Indices], where each section contains rows of tab-separated values.
Each row in the Resources section consists of four columns: Name, Type, Format, and Value. It is used to define Adapter Read settings and the type of index kit (whether a fixed layout with single- or multi- plate or non fixed layout). In addition, the mappings of well positions and index names (only for a fixed layout kit) should be included in this section (see No 5 in the table below).
Index1 and Index2 sequences should be defined in this section. Each row consists of three columns: Name, Sequence, IndexReadNumber.
| No | Field Name | Field Value |
|---|---|---|
| No | Name | Type | Format | Value |
|---|---|---|---|---|
| Name | Sequence | IndexReadNumber |
|---|---|---|
Name
Name of the kit. It is an internal name, which has to be unique within a domain.
DisplayName
Display name of the kit. It is used for the index kit display label in the Run Planning.
Organization
Organization name. It is informational and not used in planned run creation.
AllowedIndexStrategies
The index strategies supported by the kit. See AllowedIndexStrategies.
AdapterSequenceRead1
Adapter sequence for Read 1. Remove the line if it is not applicable.
AdapterSequenceRead2
Adapter sequence for Read 2. Remove the line if it is not applicable.
IndexSequences
i7Index1
A section of Index1 sequences. See IndexSequences.
IndexSequences
i7Index2
A section of Index2 sequences. See IndexSequences.
Settings
DefaultIndexStrategy
The default index strategy. It should be one of the strategy defined in the AllowedIndexStrategies.
Settings
FixedLayout
Indicates if the kit has a fixed-layout (true) or not (false). See example 3.
Settings
Multiplate
Settings
FixedIndexPositions
A section containing mappings of well position to index names. It is only applicable for a fixed-layout kit. See Settings - FixedIndexPositions.
Settings
AllowVariableLengthIndexSequences
Indicates if the kit can have index sequences with different lengths. See Settings - AllowVariableLengthIndexSequences
Settings
EnableCustomIndexCycles
Indicates if the kit uses a custom Override Cycles. See OverrideCycles.
Settings
OverrideCycles
The custom pattern for the Override Cycles. See OverrideCycles.
Settings
NumCyclesIndex1Override
Used to override the default Index1 cycles. See OverrideCycles.
Settings
NumCyclesIndex2Override
Used to override the default Index2 cycles. See OverrideCycles.
Settings
CustomBclConvertSettings
A section of custom BCL Convert settings. See Settings - CustomBclConvertSettings.
1
Name
Name of the kit. It is an internal name, which has to be unique within a domain.
2
DisplayName
Display name of the kit. It is used for the index kit display label in the Run Planning.
3
Description
Description of the kit. It is displayed below the index kit field when the kit is selected in the Run Planning.
4
IndexStrategy
The index strategies supported by the kit. See 4.1 - 4.7 for the supported values.
4.1
NoIndex: only allow No Index
4.2
SingleOnly: only allow Single Index
4.3
DualOnly: only allow Dual Indexes
4.4
NoAndSingle: allow No Index and Single Index; defaut is No Index
4.5
NoAndDual: allow No Index and Dual Indexes; default is No Index
4.6
SingleAndDual: allow Single Index and Dual Indexes; default is Single Index
4.7
All: allow No Index, Single Index and Dual Indexes; default is No Index
1
Adapter
Adapter
string
The Adapter sequence for Read 1.
2
AdapterRead2
AdapterRead2
string
The Adapter sequence for Read 2. Include this line only when applicable.
3
FixedLayout
FixedLayout
bool
Indicates if it is a fixed layout kit. Value is true or false.
4
Multiplate
Multiplate
bool
Indicates if it is a fixed layout kit with multi- or single- plate. Value is true or false.
5
{Well position name}
FixedIndexPosition
string
Index1 and Index2 names separated by a dash, e.g. D701-D501.
{Index name}
{Index sequence}
Value is 1 (for Index1) or 2 (for Index2)