Pipeline for genome assembly using MinION data.
First, the barcoded sequences are demultiplexed using Deepbinner and basecalled using Albacore (Oxford Nanopore Technologies, Oxford, UK). Nanoplot  is used to assess the quality of the sequencing data for downstream processing. If the data have sufficient quality, they are used for assembly using, e.g., Canu . Confidence on the resulting consensus assembly is obtained using Minimap2. The assembly is polished to remove common mistakes using Nanopolish, and then Circlator  is used to determine the zero-based start of the genome, which depends on whether it is a bacterial sequence or a bacteriophage sequence. Finally, the assembled genome is annotated using Prokka . Please refer to S1 Text for further details.