Pipeline for genome assembly using MinION data.

First, the barcoded sequences are demultiplexed using Deepbinner[11] and basecalled using Albacore (Oxford Nanopore Technologies, Oxford, UK). Nanoplot [12] 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 [13]. Confidence on the resulting consensus assembly is obtained using Minimap2[14]. The assembly is polished to remove common mistakes using Nanopolish[15], and then Circlator [16] 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 [17]. Please refer to S1 Text for further details.