2-AIN-505, 2-AIN-251: Seminár z bioinformatiky (1) a (3)
Zima 2017

Robert Vaser, Ivan Sovic, Niranjan Nagarajan, Mile Sikic. Fast and accurate de novo genome assembly from long uncorrected reads. Genome research, 27(5):737-746. 2017.

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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.