De novo yeast genome assemblies from MinION, PacBio and MiSeq platforms

Abstract

Long-read sequencing technologies such as Pacific Biosciences and Oxford Nanopore MinION are capable of producing long sequencing reads with average fragment lengths of over 10,000 base-pairs and maximum lengths reaching 100,000 base- pairs. Compared with short reads, the assemblies obtained from long-read sequencing platforms have much higher contig continuity and genome completeness as long fragments are able to extend paths into problematic or repetitive regions. Many successful assembly applications of the Pacific Biosciences technology have been reported ranging from small bacterial genomes to large plant and animal genomes. Recently, genome assemblies using Oxford Nanopore MinION data have attracted much attention due to the portability and low cost of this novel sequencing instrument. In this paper, we re-sequenced a well characterized genome, the Saccharomyces cerevisiae S288C strain using three different platforms: MinION, PacBio and MiSeq. We present a comprehensive metric comparison of assemblies generated by various pipelines and discuss how the platform associated data characteristics affect the assembly quality. With a given read depth of 31X, the assemblies from both Pacific Biosciences and Oxford Nanopore MinION show excellent continuity and completeness for the 16 nuclear chromosomes, but not for the mitochondrial genome, whose reconstruction still represents a significant challenge.

Figure 1

Read length distributions for the ONT and PacBio datasets. Read length distributions for the four yeast strains, S288C, N44, CBS432 and SK1 of the 2D-Pass ONT datasets in (a) and the PacBio datasets in (b). Comparison of read length distributions for the S288C strain of the 31X datasets ONT 2D-Pass and PacBio ONT-emulating 31X-subset in (c).

Figure 2

Homomer counts. Counts for the 5 bases homomers in the Reference (blue), in the Canu assembly (orange), and in the Canu assembly after polishing with Nanopolish (green).

Figure 3

Chromosome homomer rate with respect to that of the mitochondrial genome. Ratios of 5–homomer counts normalized by the chromosome length between each chromosome and the mitochondrial genome (mt).