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

BackgroundOxford Nanopore Technologies MinION sequencer is a compact, USB-powered device that has been available since 2014. Since the release of the earliest model, the throughput and error rate of the platform have improved dramatically and it has become possible to consider sequencing and assembly of eukaryotic organisms using a single nanopore flow cell. 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. FindingsDNA extracted from leaves of A. thaliana Col-0 was sequenced on two MinION flow cells, together amounting to 115x coverage of the 135 Mb genome. Reads were assembled and polished using several bioinformatics pipelines for nanopore sequence data. We performed CpG methylation analysis directly from the nanopore data, and this correlated well with a previously published bisulfite dataset. ConclusionsOur results suggest that a single MinION flow cell can generate sufficient data to assemble a genome of 135Mb, indicate functional elements, and unlock genomics for researchers of novel species from $600 in under 5 days. 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, 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. HighlightWe evaluate the effect of recent nanopore chemistry and software improvements on the ability to assemble a complete genome and conduct methylation analysis using data from a single MinION flow cell.