BCL File – What is .bcl file and how to open it?

Definition of a BCL File

A BCL (Illumina Base Call File) file is a proprietary format used to store raw sequencing data generated by Illumina’s sequencing platforms. It contains the base calls, quality scores, and other metadata associated with the sequencing run. BCL files are essential for performing downstream analysis and alignment of sequencing reads.

Structure and Content of a BCL File

BCL files are organized into two primary sections: the header and the data. The header contains information about the sequencing run, such as the instrument model, flow cell ID, and run parameters. The data section stores the base calls, quality scores, and other sequencing metrics. The data is encoded using a binary format, which optimizes file size and processing efficiency. Each base call is represented by a 16-bit integer, while the quality score is a 6-bit integer. Additional information, such as the read length, cycle number, and base quality, is also included in the data section.

Opening BCL Files Using Illumina Software

Illumina provides dedicated software for working with BCL files, such as BaseSpace Sequence Hub and Illumina Sequencing Analysis Viewer (SAV). These programs enable users to import, view, and analyze BCL data. They offer features for quality control, data filtering, and alignment to reference genomes.

To open a BCL file using Illumina software, simply drag and drop the file into the program’s interface. The software will automatically detect and parse the BCL file, displaying its contents in an intuitive graphical user interface. Users can then perform various operations on the data, such as quality assessment, alignment, and variant calling.

Converting BCL Files to FASTQ Format

For compatibility with third-party software and analysis tools, it may be necessary to convert BCL files to the widely accepted FASTQ format. Illumina provides the bcl2fastq2 conversion utility, which can be used to perform this task. The utility is available as a command-line tool or as part of the Illumina software suite.

To convert a BCL file to FASTQ using bcl2fastq2, simply run the following command:


bcl2fastq2 --input-dir <input_directory> --output-dir <output_directory>


where <input_directory> contains the BCL files and <output_directory> is the destination for the FASTQ files. Once the conversion is complete, the FASTQ files can be imported into other software tools for further analysis.

Format and Content

The Binary Call Format (BCF) is a file format used to store sequencing data from Illumina sequencing platforms. It is a lossless compression format that retains all the information from the original sequencing data, including base calls, quality scores, and alignment information. BCL files are typically very large, ranging from several gigabytes to several terabytes in size.

The BCF format is divided into three sections: the header, the sequence data, and the quality data. The header contains information about the sequencing run, such as the date, time, and instrument used. The sequence data contains the base calls for each read, encoded in a binary format. The quality data contains the quality scores for each read, also encoded in a binary format.

Applications

BCF files are used as the input to a variety of downstream analysis tools, such as alignment, assembly, and variant calling. The BCF format is also used for data storage and archival, as it is a lossless compression format that retains all the information from the original sequencing data.

Limitations

One of the limitations of the BCF format is that it is not a human-readable format. This means that it is difficult to inspect the contents of a BCF file without using a specialized tool. Additionally, the BCF format is not a widely supported format, which can make it difficult to find tools that can read and write BCF files.

Other Extensions