Our customers have long-relied on the bcl2fastq for demultiplexing sequencing data and converting base call files (BCL) into FASTQ files. While a tried and true solution, it is rather long-in-the-tooth and not as performant as we would like.
The Illumina DRAGEN Bio-IT Platform provides a superior solution to bcl2fastq in terms of speed and scale, enabling parallel processing of a greater number of multiplexed samples. In addition, DRAGEN pipelines are able to input BCL files directly, optionally skipping output of FASTQ to directly export BAM (or CRAM) files as the mapper output. While all of these are great features, we recognize that not all of our customers have access to DRAGEN’s capabilities.
Today we are excited to announce general availability of Illumina BCL Convert, a standalone local software app that converts the Binary Base Call (BCL) files produced by our sequencing systems to FASTQ files. BCL Convert is based on the same high-quality and performant codebase from DRAGEN, minus the FPGA acceleration. This means that the BCL Convert software can run on any computer running the CentOS 7 Linux operating system. In addition to demultiplexing and conversion, BCL Convert provides adapter handling (through masking and trimming) and UMI trimming. Finally BCL Convert provides QC metric files for demultiplexing, index hopping, and adapter metrics. You can read more about the BCL Convert runtime options and output in the documentation.
Start using the new BCL Convert software application by downloading it from our support site today!
P.S. –if you currently use bcl2fastq, you may be wondering what the differences are to BCL Convert. You can find this information on the BCL Convert Compatible Products support webpage.
BCL Convert is for research use only.