Fast and accurate de novo genome assembly from long uncorrected reads

Abstract

The assembly of long reads from Pacific Biosciences and Oxford Nanopore Technologies typically requires resource-intensive error-correction and consensus-generation steps to obtain high-quality assemblies. We show that the error-correction step can be omitted and that high-quality consensus sequences can be generated efficiently with a SIMD-accelerated, partial-order alignment-based, stand-alone consensus module called Racon. Based on tests with PacBio and Oxford Nanopore data sets, we show that Racon coupled with miniasm enables consensus genomes with similar or better quality than state-of-the-art methods while being an order of magnitude faster.

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

“…Therefore, Miniasm requires four rounds of Quiver polishing (Chin et al 2013) before the assembly quality converges, whereas Canu requires only a single polishing round and is ultimately fastest to generate a polished assembly (Table 1; Supplemental Note 9; Supplemental Tables S8-S11). To test if Miniasm polishing could be accelerated using a different algorithm, we tested the recently released Racon tool (Vaser et al 2017), which was designed for this purpose. However, on C. elegans, two rounds of Racon required 60 CPU hours and produced a lower-quality consensus than a single round of Quiver, which required a comparable 110 CPU hours.…”

New advances in sequence assembly

“…However, the massive read lengths and increased error rate of these new technologies have also required updated assembly methods. This issue includes three new assembly tools designed specifically for long-read PacBio and Nanopore data: Canu , HINGE (Kamath et al 2017), and Racon (Vaser et al 2017).…”

The complex architecture of plant transgene insertions

“…We performed nanopore sequencing on each line using a single R9.4 flow cell (Table 1 and Supplementary Table 1) and assembled each genome using minimap/miniasm followed by three rounds of racon [25] and one round of Pilon [26]. We assembled the three lines into 40 contigs (Col-0; longest 16 Table 2).…”