Fig. 4
From: MicroPIPE: validating an end-to-end workflow for high-quality complete bacterial genome construction
Overall pipeline: Stages and default tools in MicroPIPE. Stages in bold and italics are mandatory. All other pipeline steps are optional (users can start from fast5 or basecalled fastq files). Time for running each step is provided based on running 12 multiplexed E. coli samples with MicroPIPE v0.8. Basecalling (Guppy) and long-read polishing (Racon and Medaka) can be run on a GPU node. The rest of the pipeline is run using CPU resources. Fast = Guppy fast basecalling mode, hac = Guppy high accuracy basecalling mode. h = hour, min = minute