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Ratatosk: hybrid error correction of long reads enables accurate variant calling and assembly.

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.

SUBMITTER: Holley G

PROVIDER: S-EPMC7792008 | biostudies-literature | 2021 Jan

REPOSITORIES: biostudies-literature

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Ratatosk: hybrid error correction of long reads enables accurate variant calling and assembly.

Holley Guillaume G Beyter Doruk D Ingimundardottir Helga H Møller Peter L PL Kristmundsdottir Snædis S Eggertsson Hannes P HP Halldorsson Bjarni V BV

Genome biology 20210108 1

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 yiel ...[more]

PMID: 33419473

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