A Comparison of Nanopore Data Types, Basecalling, and Assembly Algorithms: Whole Plant Genome Assembly and Methylation Analysis from a Single MinION Flowcell

Background: Oxford Nanopore Technologies' MinION sequencer is a compact, USB-powered device that has been available, initially as part of an early-access programme, since 2014. Since the release of the earliest model, the throughput and error rate of the platform have improved dramatically and it has recently become possible to consider sequencing and assembly of eukaryotic organisms using only nanopore data. Here, we present MinION sequence data,assembly and methylation analysis for the Columbia (Col-0) accession of the model plant Arabidopsis thaliana. Further, we demonstrate the effect that recent developments (specifically the Q20+ chemistry and basecaller improvements) have had on read accuracy and assembly quality. Findings: DNA extracted from leaves of A. thaliana Col-0 was sequenced on X MinION flow cells, together amounting to x coverage of the 135 Mb genome. Y flow cells were prepared using a standard library protocol targeting an 8 kb insert, while Z flow cells were prepared with a longer insert size of ~ Z kb. Reads were assembled using Canu and a polished assembly produced using nanopolish. Our CpG methylation nanopore data and correlated well with previously published bisulfite dataset. Conclusions: Our results suggest that a single MinION flow cell can generate sufficient data to assemble a genome up to 135Mb, indicate functional elements, and unlock genomics for researchers of novel species from $Y. Here we release the full nanopore read sets for both flow cells, together with the nanopore-only assemblies. The data presented here is expected to be of particular interest to those in the Arabidopsis community, and to those looking to designing genome projects (with functional annotations), expanding our understanding of epigenetics across the tree of life, and for designing university or high school practicals teaching genomics and epigenomics. develop assembly strategies for eukaryotic organisms.