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ScaleBio tools

In addition to third-party and open-source software the workflow also uses executable tools developed by ScaleBio:

  • bc_parser
    • Extracts and error corrects cell-barcodes and UMIs from the original (input) fastq files
    • Splits (demultiplexes) the input fastq files into sample fastq files based on cell-barcodes (TN5)
    • Barcode and read-level metrics
  • sc_dedup
    • BAM deduplication aware of the multi-level combinatorial cell-barcodes.
    • Barcode and read-level metrics.

Installation

These tools are included in the scaleMethyl docker container image; when running the workflow with -profile docker (or another container engine, such as singularity, podman etc.), they will be automatically available.

These tool are however currently not available through Conda, so if running without a container system, they need to be installed first. A download script to get static pre-compiled binaries for linux (x86_64) is included; Simply run:

/PATH/TO/ScaleMethyl/envs/download-scale-tools.sh

This will install the binaries in ScaleMethyl/bin (inside the Nextflow workflow directory), from where they will be available during workflow execution.