Run Requirements

BCL Convert BCL Convert app requires the following files to be present in the run folder to complete analysis:

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BCL files (*.bcl, *.cbcl)

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Filter files (*.filter)

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Position files (*.locs, *.clocs, *s.locs)

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Aggregated files (*.bci)

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Run info file (*.xml)

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Config.xml—The config.xml file is only required for data produced by some systems. See the BCL Convert pages on the Illumina support site for more information.

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SampleSheet.csv—Supports sample sheets v1 and v2. See Sample Sheet for more details.

Sequencing Data

BCL Convert requires the following files to run. Different inputs might be required based on the sequencing system used to produce the data.

Input	Description
Base call files (*.bcl.bgzf)	Base call (BCL) files are compressed with the gzip (.gz) or blocked GNU zip (.bgzf) format.
Base call index files (*.bci)	Base call index files (BCI) files contain one record per lane in binary format. BCI files are acceptable as input by BCL Convert but are not used for analysis.
Concatenated base call files (*cbcl)	Concatenated base call (CBCL) files contain aggregated BCL data. Tiles from the same lane and surface are aggregated into one CBCL file for each lane and surface.
Filter files (*.filter)	Filter files are binary files that specify whether a given cluster passed filter.
Location files (*.locs, s.locs)	Location files (LOCS) are binary files that contain the cluster positions on the flow cell. CLOCS files are compressed versions of LOCS files.
Run information file (RunInfo.xml)	The run information file resides at the root level of the output folder. The file contains the run name, number of cycles, whether a read is an Index Read, and the number of lanes, swaths and tiles. If this file does not exist in the output folder, the software produces an error.
Configuration file (*.xml)	The configuration file resides in the BaseCalls folder and contains metadata on the sequencing run. The file is in XML format.