Run Output Files
Refer to the following sections for information on the run output files available in ElemBio Cloud.
Sequencing Run Output Files
The following table defines the sequencing run output files from an AVITI System. Using the data management tools in ElemBio Cloud, you can access the output files from runs that use a compatible storage connection.
| Directory and File Name | Format | Description | Quantity |
|---|---|---|---|
Root/Alignment/{read}_{tile}.aln | Binary files | Indicate which polonies align to PhiX Control | One per tile per read |
Root/BaseCalls/{read}_C{cycle:000}.zip | Binary files | Contain base calls and associated Q scores | One per read and cycle |
Root/Filter/{tile}.filter | Binary files | Contain the filter status for each polony | One per tile |
Root/IndexAssignment.csv | CSV | Records the results of onboard demultiplexing | One per run |
Root/Location/{tile}.loc | Binary files | Identify polony locations on the flow cell | One per tile |
Root/RunManifest.csv | CSV | Records biological sample information and analysis settings | One per run |
Root/RunManifest.json | JSON | Reserved for Element processes | One per run |
Root/RunParameters.json | JSON | Records information about the run configuration | One per run |
Stats/AvitiRunStats.json | JSON | Records run metrics | One per run |
Root/RunUploaded.json | JSON | The last file transferred and marks run completion | One per run |
Root/RunThumbnail.png | PNG | Thumbnail image for the run | One per run |
Example Files
The following table provides links to examples of key output files from sequencing runs for different versions of AVITI OS.
| AVITI OS Version | Run Metrics | Run Parameters | Run Uploaded |
|---|---|---|---|
| 2.6.0 | AvitiRunStats.json (v2.0.0) | RunParameters.json (v5.0.0) | RunUploaded.json (v1.0.0) |
| 2.5.0 | AvitiRunStats.json (v2.0.0) | RunParameters.json (v4.0.0) | RunUploaded.json (v1.0.0) |
Run Metrics (AvitiRunStats.json)
The AvitiRunStats.json file contains the source information for run metrics. You can leverage the data in this file to set up the integration of metrics into another system, such as a LIMS interface.
The file defines aggregate run metrics first, followed by read and read cycle metrics. The file then defines the same metrics for each lane, including read and read cycle metrics for the lane.
Fields
The following table describes the information in the AvitiRunStats.json file.
| Field | Description |
|---|---|
A | Base composition percentage for adenine in a cycle |
AverageQScore | Average Q score for a cycle |
BaseComposition | Identifies the set of base composition measurements for a cycle |
C | Base composition percentage for cytosine in a cycle |
Cycle | The cycle number for a set of information and metrics |
Cycles | Identifies the set of cycles for a read |
G | Base composition percentage for guanine in a cycle |
I1 | The unassigned sequence identified in the I1 read |
I2 | The unassigned sequence identified in the I2 read |
IndexAssignment | Identifies the set of information and metrics that describe index assignment for a lane or the entire run |
IndexSamples | Identifies the set of information and metrics for index samples and unassigned sequences |
Lane | The lane number for a set of per lane metrics |
LaneStats | Identifies the sets of information and metrics for lanes |
PercentAssignedReads | The percentage of reads assigned to a sample |
PercentMismatch | The percentage of polonies assigned to a sample with a mismatch |
PercentOcurrence | The occurrence rate for an unassigned sequence |
PercentPhixErrorRate | The percentage of control reads that do not align to the PhiX Control Library |
PercentPF | The percentage of reads that pass the quality filter process |
PercentQ30 | The percentage of ≥ Q30 Q scores for the run, including assigned and unassigned reads |
PercentQ40 | The percentage of ≥ Q40 Q scores for the run, including assigned and unassigned reads |
PercentQ50 | The percentage of ≥ Q50 Q scores for the run, including assigned and unassigned reads |
PFCount | The total number of reads that pass the quality filter process |
PhiXAlignmentRate | The percent of reads that align to the PhiX Control Library |
PolonyCount | The total number of polonies counted, either for a lane or the entire run |
Read | The read for a set of information and metrics, either R1 or R2 |
Reads | Identifies a set of information and metrics for the reads, either for a lane or for the entire run |
RunID | A universally unique identifier (UUID) assigned to the run and sourced from RunParameters.json |
RunName | A text-based run identifier sourced from RunParameters.json |
RunStats | Identifies the set of information and metrics for the entire run |
SampleName | The name for an index sample sourced from the run manifest |
T | Base composition percentage for thymine in a cycle |
TotalYield | The total yield of all reads in gigabases |
UnassignedSequences | Identifies a set of unassigned index sequences, either for a lane or the entire run |
Version | AVITI OS version number |
Run Parameters
The RunParameters.json file contains a record of the input information for a run. When evaluating run performance or troubleshooting, you can review this file to confirm the sequencing run used the correct recipe and other parameters.
Fields
The following table describes the information in the RunParameters.json file. When applicable, the Possible Enum Values column lists the specified value options for a field.
| Field | Description | Possible Enum Values |
|---|---|---|
AdvancedSettings | Indicates if the run uses Advanced Run Settings | Not applicable |
AnalysisLanes | The lanes that the run uses |
|
BarcodeStr | The barcode number for a consumable, which the instrument scans and identifies during consumable loading | Not applicable |
Buffer | Identifies a set of information that describes the buffer for the run | Not applicable |
ChemistryVersion | The chemistry version of the sequencing kit for the run |
|
Consumables | Identifies the set of information for run consumables | Not applicable |
Cycles | Identifies the set of cycles for the run | Not applicable |
Date | Timestamp for the run | Not applicable |
Expiration | The expiration timestamp for a consumable, which the instrument identifies or a user inputs during consumable loading | Not applicable |
ExpirationStr | An expiration ID number for a consumable, associated with the expiration date | Not applicable |
FileVersion | The version of the RunParameters.json file for the run | Not applicable |
Flowcell | Identifies a set of information that describes the flow cell for the run | Not applicable |
FlowcellID | A serial number that serves as a unique identifier for the flow cell | Not applicable |
I1 | The number of cycles in the I1 read | Not applicable |
I2 | The number of cycles in the I2 read | Not applicable |
InstrumentName | The name of the instrument for the run | Not applicable |
KitConfiguration | The total number of cycles available in the kit for the run |
|
LibraryType | The structure of the input library |
|
LotNumber | The lot number for a consumable, which the instrument identifies during consumable loading before the run | Not applicable |
LowDiversity | Indicates if the run uses the Low-Diversity High-Multiplex option |
|
OperatorName | The name of the person who set up the run on the instrument | Not applicable |
PartNumber | The part number for a consumable, which the instrument scans or a user inputs during consumable loading | Not applicable |
PlatformVersion | The version of AVITI OS for the run | Not applicable |
PMGMask | A base mask used to generate the map of polonies. | Not applicable |
PreparationWorkflow | The library prep workflow |
|
R1 | The number of cycles in the R1 read | Not applicable |
R2 | The number of cycles in the R2 read | Not applicable |
ReadOrder | The order of the reads for the run | I1,I2,R1,R2 as applicable |
RecipeExecutionID | A UUID for the run recipe, which governs the stages of a sequencing run | Not applicable |
RecipeValues | Contains additional values for the recipe that the run uses, such as a filterMask value | Not applicable |
RunDescription | An optional description for the run | Not applicable |
RunFolderName | The name of the output folder that AVITI OS creates for the run | Not applicable |
RunID | A UUID assigned to the run | Not applicable |
RunName | A text-based run identifier entered | Not applicable |
RunType | The type of AVITI System run runs | Sequencing |
SerialNumber | The serial number for a consumable, which the instrument scans or a user inputs during consumable loading | Not applicable |
SequencingCartridge | Identifies a set of information that describes the sequencing cartridge for the run | Not applicable |
Side | The side of the instrument that the run uses |
|
StorageConnectionID | A UUID for the storage connection that the run uses | Not applicable |
ThroughputSelection | The output level for the run |
|
Tiles | Identifies the set of tiles on the flow cell for the run | Not applicable |
Run Uploaded
The RunUploaded.json file indicates the completion of the run. The file contains high-level information about the run and an outcome field that confirms the run outcome. AVITI OS always transfers this file last, allowing its creation to serve as a trigger to start automated downstream analysis.
Fields
The following table defines the fields in the RunUploaded.json file. When applicable, the Possible Enum Values column lists the specified value options for a field.
| Field | Description | Possible Enum Values |
|---|---|---|
version | The version of the RunUploaded.json file | Not applicable |
instrument | The name of the instrument for the run | Not applicable |
instrumentId | A UUID for the instrument | Not applicable |
outcome | The final outcome of the run |
|
runType | The type of AVITI System run | Sequencing |
recipeExecutionId | A UUID for the run recipe and sourced from RunParameters.json | Not applicable |
runID | A UUID assigned to the run and sourced from RunParameters.json | Not applicable |