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Pipeline for genome assembly using MinION data.

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posted on 23.01.2020, 18:24 by Alex N. Salazar, Franklin L. Nobrega, Christine Anyansi, Cristian Aparicio-Maldonado, Ana Rita Costa, Anna C. Haagsma, Anwar Hiralal, Ahmed Mahfouz, Rebecca E. McKenzie, Teunke van Rossum, Stan J. J. Brouns, Thomas Abeel

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.