Fig. 1.

Diagram of analysis process. a MinION sequencing using MinKNOW (runs outside of CRuMPIT). b Fast5 files are detected and submitted as batches for the Nextflow workflow. c Nextflow workflow which is contained within a singularity image and can be distributed across a cluster (SLURM used here) or on a local machine. d Run analysis using data pushed to a MongoDB database, this can be conducted separately on any machine with network access to the database. Each component (green or blue rounded rectangle) of CRuMPIT can be run independently from the same or different networked computers, (e) or the entire process can be run from a single program. Square rectangles represent programs, some of which are within python wrappers. Arrows represent direction of data transfer within the workflow or between componants