A single chromosome assembly of Bacteroides fragilis strain BE1 from Illumina and MinION nanopore sequencing data

Abstract

Background: Second and third generation sequencing technologies have revolutionised bacterial genomics. Short-read Illumina reads result in cheap but fragmented assemblies, whereas longer reads are more expensive but result in more complete genomes. The Oxford Nanopore MinION device is a revolutionary mobile sequencer that can produce thousands of long, single molecule reads.

Results: We sequenced Bacteroides fragilis strain BE1 using both the Illumina MiSeq and Oxford Nanopore MinION platforms. We were able to assemble a single chromosome of 5.18 Mb, with no gaps, using publicly available software and commodity computing hardware. We identified gene rearrangements and the state of invertible promoters in the strain.

Conclusions: The single chromosome assembly of Bacteroides fragilis strain BE1 was achieved using only modest amounts of data, publicly available software and commodity computing hardware. This combination of technologies offers the possibility of ultra-cheap, high quality, finished bacterial genomes.

Fig. 1

MinION read-length histogram. A histogram of 2D read lengths from 7300 MinION reads. The peak at 3-4kb represents the lambda spike-in

Fig. 2

MinION percentage identity. A boxplot of percentage identity to our assembly for 7300 MinION reads

Fig. 3

MinION alignment length. A boxplot showing the ratio of alignment length to read length for 7300 MinION reads

Fig. 4

MUMmer comparison. A plot from MUMmer comparing NC_003228 (y-axis) with our assembly (x-axis) using MUMmer and nucmer [30]