Sequencing Output Files - illumina NovaSeq 6000 Manual

NovaSeq 6000 Sequencing System Guide

Sequencing Output Files

File Type
Base call files
Cluster location files
Filter files
InterOp files
Run information file
Thumbnail files
Document # 1000000019358 v07Material # 20023471
For Research Use Only. Not for use in diagnostic procedures.
File Description, Location, and Name
Each cluster analyzed is included in a base call file, aggregated in one file per cycle, lane, and
surface. The aggregated file contains the base call and encoded quality score for every cluster.
The 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
For each flow cell, a binary cluster location file contains the XY coordinates for clusters in a tile. A
hexagonal layout that matches the nanowell layout of the flow cell predefines the coordinates.
Data\Intensities
s_[lane].locs
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
Binary reporting files used for Sequencing Analysis Viewer. InterOp files are updated throughout
the run.
InterOp folder
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
When enabled, a thumbnail image for every 10
Thumbnail_Images\L001\C[X.1]—Files are stored in a subfolder for each cycle.
s_[lane]_[tile]_[channel].jpg—The thumbnail image includes the tile number.
th
tile in each color channel (red and green).
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