GenPipes 4.3.0 Release Notes

What’s new?

  • MethylSeq Pipeline: Two new protocols are newly added to MethylSequencing pipeline. These protocols are based on Illumina Dragen Bio-IT Platform. The new protocols are tested on Abacus (the McGill Genome Centre HPC) and usable where a “Dragen” allocation is available.

    • bismark option uses the Bismark protocol (formerly the default protocol) to perform the whole analysis including the read alignment, de-duplication, and methylation calls.

    • dragen option uses the Dragen protocol to perform the whole analysis.

    • hybrid option uses the Dragen protocol for fast read alignment and uses Bismark for the other steps.

  • DNASeq: In the latest release, the unmapped reads in DNASeq pipeline are now extracted from the merged/sorted bam files. After the base recalibration step, the unmapped reads are re-injected into the fastq.

    This ensures that the unmapped reads are available for further analysis, if needed. Without this process, the base recalibration may eventually remove the unmapped reads.

Other Updates

  • CovSeq Pipeline: Bug fixes such as CovSeq report is now repaired for cases with multiple readsets per sample.

  • The .ini files are now standardized.

Quick! Where can I find it? I can’t wait!

Where is the detailed ChangeLog?

A ChangeLog ( is available in the archive as well as in the repository.

Since we use git, there are many ways to get the details in many formats. One of our preferred ways is to use a script written by the author of the Ray assembler: Sébastien Boisvert, which lists the commits by tag and author:

Enjoy our pipelines on the many clusters where they are installed!