1 The bcl2Fastq software

The bcl2Fastq software converts basecalls from Illumina High Throughput Sequencing (HTS) machines to fastQ files containing sequence information ready for further analysis.

The conversion of basecalls using the bcl2Fastq software requires multiple input files and parameters which allow the software to correctly basecall as well as demultiplex data into relevant samples by any index information contained within the data.

For detailed information on the latest version of bcl2Fastq software, its’ installation, its’ required input files and generated output files visit the Illumina software’s website here.

1.1 Input files for bcl2Fastq.

The bcl2Fastq software converts basecalls generated by Illumina’s Real Time Analysis (RTA) software to fastQ files. The output from RTA is presented in the directory structure below alongside the required input files runParameters.xml and a user generated SampleSheet.csv.