Fig. 1

BiocMAP workflow overview. Diagram representing the conceptual workflow traversed by BiocMAP. The red box indicates the FASTQ files are inputs to the pipeline; green coloring denotes major output files from the pipeline; the remaining boxes represent computational steps. Yellow and orange-colored steps are optional or not always performed; for example, lambda pseudoalignment is an optional step intended for experiments with spike-ins of the lambda bacteriophage. Finally, blue-colored steps are ordinary processes which occur on every pipeline execution. Depending on the available high performance computing (HPC) systems, both modules can be run sequentially on a HPC system with both GPUs and CPUs, or the alignment module can be run on a GPU-powered HPC system, then files transferred to a CPU-based HPC system as well as updating file paths on the rules.txt file (dotted line), before running the extraction module on the CPU-based HPC system