A major challenge to long read sequencing data is their high error rate of up to 15%. We present Ratatosk, a method to correct long reads with short read data. We demonstrate on 5 human genome trios that Ratatosk reduces the error rate of long reads 6-fold on average with a median error rate as low as 0.22 %. SNP calls in Ratatosk corrected reads are nearly 99 % accurate and indel calls accuracy is increased by up to 37 %. An assembly of Ratatosk corrected reads from an Ashkenazi individual yields a contig N50 of 45 Mbp and less misassemblies than a PacBio HiFi reads assembly.
CITATION STYLE
Holley, G., Beyter, D., Ingimundardottir, H., Møller, P. L., Kristmundsdottir, S., Eggertsson, H. P., & Halldorsson, B. V. (2021). Ratatosk: hybrid error correction of long reads enables accurate variant calling and assembly. Genome Biology, 22(1). https://doi.org/10.1186/s13059-020-02244-4
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