Fast and accurate de novo genome assembly from long uncorrected reads
- 1 University of Zagreb, Faculty of Electrical Engineering and Computing;
- 2 Rudjer Boskovic Institute;
- 3 Genome Institute of Singapore
- ↵* Corresponding author; email: mile.sikic{at}fer.hr
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 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.
- Received August 5, 2016.
- Accepted January 17, 2017.
- Published by Cold Spring Harbor Laboratory Press
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