Primary sequencing output of an Illumina sequencer are per-cycle base call (bcl) files, which first need to be converted to fastq format, so that the data can be pushed to downstream applications. The conversion tool implemented in Partek Flow is Illumina's bcl2fastq Conversion Software. In addition to the file conversion, bcl2fastq tool also demultiplexes the bcl files in the same step and, hence, outputs demultiplexed fastq files as the primary result. The bcl2fastq application also supports two optional tasks: adapter trimming and removal of unique molecular identifier (UMI) sequences.

To base a new project on bcl files, first select Import data option on the Data tab and then push the Import bcl files button. The resulting window shows the configuration dialog (Figure 1).