Input files

The input files Bases2Fastq™ reads, and when each one is used.

Input files for AVITI and AVITI24 sequencing

The following table lists the input files for Bases2Fastq. Bases2Fastq only uses the alignment file when the run manifest setting SpikeInAsUnassigned is set to True.

File	Directory and File Name	Description	Quantity
Alignment	Root/Alignment/{read}_{tile}.aln	Binary files that indicate which polonies align to the PhiX Control Library	One per tile per read
Bases	Root/BaseCalls/{read}_C{cycle:000}.zip	Binary files that contain base calls and the associated Q scores	One per read and cycle
Filter	Root/Filter/{tile}.filter	Binary files that contain the filter status for each polony	One per tile
Location	Root/Location/{tile}.loc	Binary files that identify polony locations on the flow cell	One per tile
Run manifest, CSV	Root/RunManifest.csv	CSV file that records biological sample information and analysis settings	One per run
Run manifest, JSON	Root/RunManifest.json	JSON file that is reserved for Element Biosciences processes	One per run
Run parameters	Root/RunParameters.json	JSON file that records information about the run configuration	One per run

Input files for Vitari sequencing runs

Vitari™ sequencing runs store base calls as one compressed file per tile, read, and cycle in the Basecall directory. All other input files use the same layout as AVITI™ sequencing runs. Bases2Fastq only uses the alignment file when the run manifest setting SpikeInAsUnassigned is set to True.

File	Directory and File Name	Description	Quantity
Alignment	Root/Alignment/{tile}.aln	Binary files that indicate which polonies align to the PhiX Control Library	One per tile
Bases	Root/Basecall/{tile}/{read}_{tile}_C{cycle:000}.bases.gz	Compressed binary files that contain base calls and the associated Q scores	One per tile, read, and cycle
Filter	Root/Filter/{tile}.filter	Binary files that contain the filter status for each polony	One per tile
Location	Root/Location/{tile}.loc	Binary files that identify polony locations on the flow cell	One per tile
Run manifest, CSV	Root/RunManifest.csv	CSV file that records biological sample information and analysis settings	One per run
Run manifest, JSON	Root/RunManifest.json	JSON file that is reserved for Element processes	One per run
Run parameters	Root/RunParameters.json	JSON file that records information about the run configuration	One per run

Input files for cell screening

The following table lists the input files for Bases2Fastq. The target cell assignment manifest is required only when a --per-target-fastq optional argument is run.

File	Directory and File Name	Description	Quantity
Bases	Root/BaseCalling/BaseCalls/{batch}_C{cycle:000}.zip	Binary files that contain base calls and associated Q scores	One per batch and cycle
Cell segmentation	Root/CellSegmentation/	Cell segmentation masks as TIFF files or a Zarr v3 store. To use alternative masks, see --segmentation.	One per run
Filter	Root/BaseCalling/Filter/{tile}.filter	Binary files that contain the filter status for each polony	One per tile
Location	Root/BaseCalling/Location/{tile}.loc	Binary files that identify the polony locations on the flow cell	One per tile
Panel	Root/Panel.json	JSON file that records the panel and batch configuration for the run	One per run
Run manifest, CSV	Root/RunManifest.csv	CSV file that records biological sample information and analysis settings	One per run
Run manifest, JSON	Root/RunManifest.json	JSON file that is reserved for Element processes	One per run
Run Parameters	Root/RunParameters.json	JSON file that records information about the run configuration	One per run
Target Cell Assignment manifest, CSV	Root/TargetCellAssignmentManifest.csv	(Optional) CSV file that records target information	One per run
Target Cell Assignment manifest, JSON	Root/TargetCellAssignmentManifest.json	(Optional) JSON file that is reserved for Element processes	One per run