Sequencing Output Files

File Type	File Description, Location, and Name
Concatenated base call files	Each cluster analyzed is included in a concatenated base call file, aggregated in one file per cycle, lane, and surface. The aggregated file contains the concatenated base call and encoded quality score for every cluster. The concatenated base call files are used by BaseSpace Sequence Hub or bcl2fastq2. Data/Intensities/BaseCalls/L001/C1.1 L[lane]_[surface].cbcl, for example L001_1.cbcl
Cluster location files	For each flow cell, a binary cluster location file contains the XY coordinates for clusters in a tile. Either a diamond or hexagonal layout that matches the nanowell layout of the flow cell predefines the coordinates. Data/Intensities s_[lane].locs
Filter files	The filter file specifies whether a cluster passed filters. Filter files are generated at cycle 26 using 25 cycles of data. For each tile, one filter file is generated. Data/Intensities/BaseCalls/L001 s_[lane]_[tile].filter
InterOp files	Binary reporting files can be viewed on-instrument with the Instrument Control Software or off-instrument in SAV or BaseSpace Sequence Hub. InterOp files are updated throughout the run. InterOp folder
Run information file	Lists the run name, number of cycles in each read, whether the read is an Index Read, and the number of swaths and tiles on the flow cell. The run info file is created at the beginning of the run. [Root folder], RunInfo.xml

Concatenated base call files

Each cluster analyzed is included in a concatenated base call file, aggregated in one file per cycle, lane, and surface. The aggregated file contains the concatenated base call and encoded quality score for every cluster. The concatenated base call files are used by BaseSpace Sequence Hub or bcl2fastq2.

Data/Intensities/BaseCalls/L001/C1.1

L[lane]_[surface].cbcl, for example L001_1.cbcl

Cluster location files

For each flow cell, a binary cluster location file contains the XY coordinates for clusters in a tile. Either a diamond or hexagonal layout that matches the nanowell layout of the flow cell predefines the coordinates.

Data/Intensities

s_[lane].locs

Filter files

The filter file specifies whether a cluster passed filters. Filter files are generated at cycle 26 using 25 cycles of data. For each tile, one filter file is generated.

Data/Intensities/BaseCalls/L001

s_[lane]_[tile].filter

InterOp files

Binary reporting files can be viewed on-instrument with the Instrument Control Software or off-instrument in SAV or BaseSpace Sequence Hub. InterOp files are updated throughout the run.

InterOp folder

Run information file

Lists the run name, number of cycles in each read, whether the read is an Index Read, and the number of swaths and tiles on the flow cell. The run info file is created at the beginning of the run.

[Root folder], RunInfo.xml