Ratatosk: hybrid error correction of long reads enables accurate variant calling and assembly
Guillaume Holley, Doruk Beyter, Helga Ingimundardóttir, Peter Möller, Snædís Kristmundsdóttir, Hannes P. Eggertsson, Bjarni V. Halldórsson
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.
Topics & Concepts
ContigIndelWord error rateSequence assemblyBiologyHybrid genome assemblyComputational biologyError detection and correctionHuman genomeGenomeReference genomeINDEL MutationComputer scienceGeneticsAlgorithmArtificial intelligenceGeneSingle-nucleotide polymorphismGenotypeTranscriptomeGene expressionGenomics and Phylogenetic StudiesChromosomal and Genetic VariationsGenomics and Rare Diseases