Fast and accurate de novo genome assembly from long uncorrected reads

By Robert Vaser, Ivan Sovic, Niranjan Nagarajan, Mile Sikic. bioRxiv, 2016

2,637 citations recorded by the source corpus.

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 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 datasets 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. Racon is available open source under the MIT license at https://github.com/isovic/racon.git.

Subfields: Artificial Intelligence, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/9d62188a0c9895b4c8b6d9c8cbb76945ee1c2a7a

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Citations in the corpus

A complete Cannabis chromosome assembly and adaptive admixture for elevated cannabidiol (CBD) content (2018, methodology): “0 and containing four or more markers were used to construct a linkage map using the Kosambi (25) function.”
What is Speciation Genomics? The roles of ecology, gene flow, and genomic architecture in the formation of species (2018, background): “Thanks to remarkable advances in sequencing technologies and de novo genome assembly (Alkhateeb & Rueda, 2017; Jackman et al., 2017; Kamath et al., 2017; Paten et al., 2017; Vaser et al., 2017; Worley, 2017), it is no longer the case that the availability of a closely related model species and refer”
Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation (2016, methodology): “TotestifMiniasmpolishingcouldbe accelerated using a different algorithm, we tested the recently released Racon tool (Vaser et al. 2017), which was designed for this purpose.”
The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities (2019, methodology): “We also provide an image of the assembly graph using Bandage (18), and assemblies can be polished using Racon (19) and Pi-lon (20) for long-and short-read assemblies respectively.”
Long-read human genome sequencing and its applications (2020, neutral): “Most of these errors can be resolved with use of polishing tools (such as Racon 48 , Nanopolish 63,85,86 , MarginPolish 36 , HELEN 36 , Quiver 46 , Arrow and Medaka) and error correction with short-read sequence data generated from the same individual 47 .”
From squiggle to basepair: computational approaches for improving nanopore sequencing read accuracy (2018, methodology): “Genome assembly tools that implement POA graphs for nanopore consensus calling and read correction include Nanocorrect [15], Racon [46], and Canu [14].”
The genome polishing tool POLCA makes fast and accurate corrections in genome assemblies (2019, methodology): “There are several software tools available for polishing assemblies with Illumina data, with the most widely used ones being Pilon [4] and Racon [5].”
Performance of neural network basecalling tools for Oxford Nanopore sequencing (2019, methodology): “Even after multiple rounds, Racon does not always converge to the best possible sequence, so we used Rebaler with an iterative approach: running the assembly multiple times, each time with shuffled input reads and a rotated (shifted start position) reference genome.”