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. Partek^® Flow^® software comes with a conversion tool that can be used to import data in the bcl file format . In addition to the file conversion, this tool also demultiplexes the bcl files in the same step and outputs demultiplexed fastq files as the result.

We recommend you start by transferring the entire Illumina run folder to the Partek Flow server. To start a new project with 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).

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The bcl files hold the base calls and are in the Data directory within the whole Illumina run folder. Note that the Data directory file path needs to point to the directory, not to an individual bcl file. 

The RunInfo.xml file is generated by the primary analysis software and contains information on the run, flow cell, the instrument, the time stamp, and the read structure (number of reads, number of cycles per read, whether a read is an index read). This file is typically stored at the top level in the Illumina run folder.

The SampleSheet.csv file provides the information on the relationship between the samples and indices specified during library creation. Although it has four sections, two sections (Settings and Data) are important for the data import and conversion. Finally, the bcl files hold the base calls and are contained within the BaseCalls directory (note that the Select base calls directory option needs to point to the directory, not to an individual bcl file). For  For more information on the files, consult Illumina documentation.

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