What are BCL files for?

[dawe]

HI all,
we've just switched to SCS 2.8 and we have now BCL files from RTA... I see I must convert them to qseq if I want to run GERALD (or any other downstream application), so I wonder what is this file format for...
d

[kmcarr]

.bcl files are base calls per cycle, a binary file containing base call and quality for each tile in each cycle. The advantage of this is that base calling is happening "on the fly", as opposed to waiting until the run is over and calling bases for the entire read.

Currently the CASAVA tools only take whole reads as input so the files must be converted to qseq. I have heard from Illumina reps that future versions of CASAVA will be able to use .bcl files directly for input, obviating the need for the conversion step.