zymoresearch/bcl2fastq repository overview

⁠Supported tags and respective Dockerfile links

• 2.20⁠

⁠What is bcl2fastq?

The Illumina bcl2fastq2 Conversion Software demultiplexes sequencing data and converts base call (BCL) files into FASTQ files. For more information, please see the latest software guide⁠.

This image is built based on Alpine Linux. It's very lightweight with only 36M in size.

⁠How to use this image

In the following examples, the -d option of the docker run command will run container in background. Please use docker logs -f <container name> to fetch the container log.

⁠Demultiplex to the same run folder

$ docker run -d -v <runfolder-dir>:/mnt/run zymoresearch/bcl2fastq --runfolder-dir /mnt/run

Replace <runfolder-dir> with the real run folder directory on the host machine.

⁠Demultiplex to a different location

This is useful when FASTQ files need to be demultiplexed and stored separately e.g. in a NAS storage device.

$ docker run -d -v <runfolder-dir>:/mnt/run -v <output-dir>:/mnt/output zymoresearch/bcl2fastq \
      --runfolder-dir /mnt/run --output-dir /mnt/output

Replace <runfolder-dir> and <output-dir> with the corresponding directories on the host machine.