Sequencing Output Files

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.

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

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