Sequencing Run Output Files

The following is a representative run output directory of a successful sequencing run:

example-storage-location
└── DemoInstrumentName
    └── 20240506_DemoInstrumentName_ExampleRunName-2x150CloudBreakAdept
        ├── Alignment
        ├── AvitiRunStats.json
        ├── BaseCalls
        │   ├── I1_C001.zip ... for n cycles
        │   ├── I2_C001.zip ...for  n cycles
        │   ├── R1_C001.zip ... for n cycles
        │   ├── R2_C001.zip ... for n cycles
        ├── Filter
        ├── Location
        ├── RunManifest.csv
        ├── RunManifest.json
        ├── RunParameters.json
        ├── RunThumbnail.png
        ├── RunUploaded.json
        └── Stats
            └── run.prodstats

Output Files

The following table defines the sequencing run output files from an AVITI System. Using the data browsing tools in ElemBio Cloud, you can access the output files from runs that use a compatible storage connection.

Braces around a file name component indicate variability. For example, the value for {tile} depends on the applicable tile number.

Directory and File Name	File Format	Description	Quantity
Root/Alignment/{read}_{tile}.aln	Binary	Indicate which polonies align to PhiX Control	One per tile per read
Root/BaseCalls/{read}_C{cycle}.zip	Binary	Contain base calls and associated Q scores	One per read and cycle
Root/Filter/{tile}.filter	Binary	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	Identify polony locations on the flow cell	One per tile
Root/Panel/{file}.bed	BED	Identifies the bed panel; Only found in Trinity runs	One per run
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.

Field	Description	Allowed Values
AdvancedSettings	Indicates if the run uses Advanced Run Settings	Not applicable
AnalysisLanes	The lanes that the run uses	1 2 1+2
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	Cloudbreak for Cloudbreak CloudbreakFS for Cloudbreak Freestyle CloudbreakUQ for Cloudbreak UltraQ
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	150Cycles for a 2 x 75 kit 300Cycles for a 2 x 150 kit 600Cycles for a 2 x 300 kit
LibraryType	The structure of the input library	Circular Linear
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	true false
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	Adept Elevate ThirdParty
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	SideA SideB
StorageConnectionID	A UUID for the storage connection that the run uses	Not applicable
ThroughputSelection	The output level for the run	High Medium Low
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. the Allowed Values column lists the specified value options for a field.

Field	Description	Allowed 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	OutcomeCompleted OutcomeStopped OutcomeFailed
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