In addition to third-party and open-source software the workflow also uses several 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 (tagmentation wells)
- Barcode and read-level metrics
- sc_dedup
- BAM deduplication aware of the multi-level combinatorial cell-barcodes
- Cell-barcode metrics
- sc_counter
- Cell-by-peak count matrix generation, used for peak and TSS counts.
- Peak metrics
These tools are included in the scaleAtac docker container image; when running the workflow in the recommended configuration with docker (or singularity, podman etc.), they will be automatically available.
These tool are however currently not available through Conda, so if running without docker, they need to be installed first. A download script to get static pre-compiled binaries for linux (x86_64) is provided in envs/download-scale-tools.sh. It will install the binaries in the bin directory inside the nextflow workflow, from where they will be available to the workflow.