Haplotype threading: accurate polyploid phasing from long reads
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 polyph...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2020-09-01
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| Series: | Genome Biology |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s13059-020-02158-1 |
| _version_ | 1818289488003072000 |
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| author | Sven D. Schrinner Rebecca Serra Mari Jana Ebler Mikko Rautiainen Lancelot Seillier Julia J. Reimer Björn Usadel Tobias Marschall Gunnar W. Klau |
| author_facet | Sven D. Schrinner Rebecca Serra Mari Jana Ebler Mikko Rautiainen Lancelot Seillier Julia J. Reimer Björn Usadel Tobias Marschall Gunnar W. Klau |
| author_sort | Sven D. Schrinner |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-13T02:13:04Z |
| format | Article |
| id | doaj.art-368ec63d77e4446d94461a2dee60f294 |
| institution | Directory Open Access Journal |
| issn | 1474-760X |
| language | English |
| last_indexed | 2024-12-13T02:13:04Z |
| publishDate | 2020-09-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj.art-368ec63d77e4446d94461a2dee60f2942022-12-22T00:02:58ZengBMCGenome Biology1474-760X2020-09-0121112210.1186/s13059-020-02158-1Haplotype threading: accurate polyploid phasing from long readsSven D. Schrinner0Rebecca Serra Mari1Jana Ebler2Mikko Rautiainen3Lancelot Seillier4Julia J. Reimer5Björn Usadel6Tobias Marschall7Gunnar W. Klau8Algorithmic Bioinformatics, Heinrich Heine University DüsseldorfInstitute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University DüsseldorfInstitute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University DüsseldorfCenter for Bioinformatics, Saarland UniversityInstitute for Biology I, RWTH AachenInstitute for Biology I, RWTH AachenForschungszentrum Jülich IBG-4Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University DüsseldorfAlgorithmic Bioinformatics, Heinrich Heine University DüsseldorfAbstract 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.http://link.springer.com/article/10.1186/s13059-020-02158-1PolyploidyPhasingHaplotypesCluster editingHigh-throughput nucleotide sequencingPlant science |
| spellingShingle | Sven D. Schrinner Rebecca Serra Mari Jana Ebler Mikko Rautiainen Lancelot Seillier Julia J. Reimer Björn Usadel Tobias Marschall Gunnar W. Klau Haplotype threading: accurate polyploid phasing from long reads Genome Biology Polyploidy Phasing Haplotypes Cluster editing High-throughput nucleotide sequencing Plant science |
| title | Haplotype threading: accurate polyploid phasing from long reads |
| title_full | Haplotype threading: accurate polyploid phasing from long reads |
| title_fullStr | Haplotype threading: accurate polyploid phasing from long reads |
| title_full_unstemmed | Haplotype threading: accurate polyploid phasing from long reads |
| title_short | Haplotype threading: accurate polyploid phasing from long reads |
| title_sort | haplotype threading accurate polyploid phasing from long reads |
| topic | Polyploidy Phasing Haplotypes Cluster editing High-throughput nucleotide sequencing Plant science |
| url | http://link.springer.com/article/10.1186/s13059-020-02158-1 |
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