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Bcl Conversion and Demultiplexing

As of CASAVA 1.8, configureAlignment uses FASTQ files as input. Since Illumina sequencing instruments generate *.bcl files as primary sequencing output, CASAVA contains a BCL to FASTQ converter that combines these per-cycle *.bcl files from a run and translates them into FASTQ files. CASAVA 1.8 can start with bcl conversion and alignment as soon as the first read has been sequenced completely.