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. 2017 May;27(5):737-746.
doi: 10.1101/gr.214270.116. Epub 2017 Jan 18.

Fast and accurate de novo genome assembly from long uncorrected reads

Robert Vaser  1 , Ivan Sović  2 , Niranjan Nagarajan  3 , Mile Šikić  1   4
Affiliations

Fast and accurate de novo genome assembly from long uncorrected reads

Robert Vaser et al. Genome Res. 2017 May.

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.

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Figures

Figure 1.
Figure 1.
Racon's speedup compared with FALCON and Canu.
Figure 2.
Figure 2.
Scalability of Racon as a function of genome size. Read coverage was subsampled to be 81× (limited by the Caenorhabditis elegans data set), and the figure shows results for one iteration of Racon.
Figure 3.
Figure 3.
Overview of the Racon consensus process.
Algorithm 1.
Algorithm 1.
The Racon algorithm for consensus generation.
Algorithm 2.
Algorithm 2.
Functions for filtering mappings/overlaps in Racon.
Figure 4.
Figure 4.
Depiction of the SIMD vectorization approach used in SPOA.
Algorithm 3.
Algorithm 3.
Pseudocode for the SPOA algorithm. The displayed function aligns a sequence to a preconstructed POA graph using SIMD intrinsics. Capitalized variables are SIMD vectors. Alignment mode is Needleman-Wunsch.
See this image and copyright information in PMC

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