bioinfoipec/bcl2fastq repository overview

⁠bcl2fastq

This image facilitates the usage of bcl2fastq⁠, is a tool that converts both demultiplexes data and converts BCL files generated by Illumina sequencing systems to standard FASTQ file formats for downstream analysis.

⁠Using bcl2fastq image

In order to use this image you need to run the folliwing command: docker run --rm -v /your/data/dir:/data bioinfoipec/bcl2fastq bcl2fastq [options]

See the MANUAL⁠, for more details.

To obtain abbreviated help of an application, you just need to run: docker run --rm bioinfoipec/bcl2fastq bcl2fastq -h.

⁠Test data

To test the previous command, you can access the following link⁠.