A complete bacterial genome assembled de novo using only nanopore sequencing data

Abstract

A method for de novo assembly of data from the Oxford Nanopore MinION instrument is presented which is able to reconstruct the sequence of an entire bacterial chromosome in a single contig. Initially, overlaps between nanopore reads are detected. Reads are then subjected to one or more rounds of error correction by a multiple alignment process employing partial order graphs. After correction, reads are assembled using the Celera assembler. Finally, the assembly is polished using signal-level data from the nanopore employing a novel hidden Markov model. We show that this method is able to assemble nanopore reads from Escherichia coli K-12 MG1655 into a single contig of length 4.6Mb permitting a full reconstruction of gene order. The resulting draft assembly has 98.4% nucleotide identity compared to the finished reference genome. After polishing the assembly with our signal-level HMM, the nucleotide identity is improved to 99.4%. We show that MinION sequencing data can be used to reconstruct genomes without the need for a reference sequence or data from other sequencing platforms.