Ratatosk: hybrid error correction of long reads enables accurate variant calling and assembly
2021
Guillaume Holley | Doruk Beyter | Helga Ingimundardottir | Peter L. Møller | Snædis Kristmundsdottir | Hannes P. Eggertsson | Bjarni V. Halldorsson
Abstract 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.
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