bioinformaticssequencing

BCL files

As part of the Primary Analysis Illumina sequencing machines measure the intensity of the channels used for encoding the different bases and identify the most likely base at a given position of a sequencing read (tag). The Real Time Analysis (RTA) software writes the base and the confidence in the call as a quality score to base call (.bcl) files. As the name implies this is done in real time, i.e. for every cycle of the sequencing run a call for every location identified on the flow cell (tiles and lanes) is added. Bcl files are stored in binary format and represent the raw data output of a sequencing run. The format is described here. Software such as Casava/BclToFastq, Eland or the iSAAC aligner can make use of these files.

The *.bcl files are stored in the BaseCalls directory:

<run directory>/Data/Intensities/BaseCalls/L<lane>/C<cycle>.1

They are named in the format:

s_<lane>_<tile>.bcl

If you want to overcome errors during downstream processing from missing calls, software such as iSAAC and configureBclToFastq have an “–ignore-missing-bcl” command line option. This will interpret missing *.bcl files as no call (N) at that position.

Sources: Illumina, SeqAnswers