Haplotype threading: accurate polyploid phasing from long reads

Genome biology, vol. 21, pp. 252

Abstract

Resolving genomes at haplotype level is crucial for understanding the evolutionary history of polyploid species and for designing advanced breeding strategies. Polyploid phasing still presents considerable challenges, especially in regions of collapsing haplotypes.We present WHATSHAP POLYPHASE, a novel two-stage approach that addresses these challenges by (i) clustering reads and (ii) threading the haplotypes through the clusters. Our method outperforms the state-of-the-art in terms of phasing quality. Using a real tetraploid potato dataset, we demonstrate how to assemble local genomic regions of interest at the haplotype level. Our algorithm is implemented as part of the widely used open source tool WhatsHap.

Authors 9

1. Sven D. Schrinner

   Heinrich Heine University Düsseldorf

   Affiliation as printed

   Algorithmic Bioinformatics, Heinrich Heine University Düsseldorf, Universitätsstr. 1, Düsseldorf, 40225, Germany

2. Rebecca Serra Mari

   Heinrich Heine University Düsseldorf · Saarland University

   Affiliation as printed

   Center for Bioinformatics, Saarland University, Saarland Informatics Campus E2.1, Saarbrücken, 66123, Germany

   Graduate School of Computer Science, Saarland Informatics Campus E1.3, Saarbrücken, 66123, Germany

   Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstraße 5, Düsseldorf, 40225, Germany

3. Jana Ebler

   Heinrich Heine University Düsseldorf

   Affiliation as printed

   Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstraße 5, Düsseldorf, 40225, Germany

4. Mikko Rautiainen

   Max Planck Institute for Informatics · Saarland University

   Affiliation as printed

   Center for Bioinformatics, Saarland University, Saarland Informatics Campus E2.1, Saarbrücken, 66123, Germany

   Graduate School of Computer Science, Saarland Informatics Campus E1.3, Saarbrücken, 66123, Germany

   Max Planck Institute for Informatics, Saarbrücken, 66123, Germany

5. Lancelot Seillier Aachen Institute for Biology I

   RWTH Aachen University

   Affiliation as printed

   Institute for Biology I, RWTH Aachen, Worringer Weg 3, Aachen, 52074, Germany

6. Julia J. Reimer Aachen Institute for Biology I

   RWTH Aachen University

   Affiliation as printed

   Institute for Biology I, RWTH Aachen, Worringer Weg 3, Aachen, 52074, Germany

7. Björn Usadel Aachen Institute for Biology I

   Forschungszentrum Jülich · Cluster of Excellence on Plant Sciences · Heinrich Heine University Düsseldorf · RWTH Aachen University

   Affiliation as printed

   Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University Düsseldorf, Universitätsstr. 1, Düsseldorf, 40225, Germany

   Forschungszentrum Jülich IBG-4, Wilhelm-Johnen-Str., Jülich, 52428, Germany

   Institute for Biology I, RWTH Aachen, Worringer Weg 3, Aachen, 52074, Germany

8. Tobias Marschall corresponding

   Heinrich Heine University Düsseldorf

   Affiliation as printed

   Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstraße 5, Düsseldorf, 40225, Germany. tobias.marschall@hhu.de

   Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstraße 5, Düsseldorf, 40225, Germany

9. Gunnar W. Klau corresponding

   Cluster of Excellence on Plant Sciences · Heinrich Heine University Düsseldorf

   Affiliation as printed

   Algorithmic Bioinformatics, Heinrich Heine University Düsseldorf, Universitätsstr. 1, Düsseldorf, 40225, Germany. gunnar.klau@hhu.de

   Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University Düsseldorf, Universitätsstr. 1, Düsseldorf, 40225, Germany. gunnar.klau@hhu.de

   Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University Düsseldorf, Universitätsstr. 1, Düsseldorf, 40225, Germany