Haplotype-aware diplotyping from noisy long reads

Abstract Current genotyping approaches for single-nucleotide variations rely on short, accurate reads from second-generation sequencing devices. Presently, third-generation sequencing platforms are rapidly becoming more widespread, yet approaches for leveraging their long but error-prone reads for g...

Full description

Bibliographic Details
Main Authors:	Jana Ebler, Marina Haukness, Trevor Pesout, Tobias Marschall, Benedict Paten
Format:	Article
Language:	English
Published:	BMC 2019-06-01
Series:	Genome Biology
Subjects:	Computational genomics Long reads Genotyping Phasing Haplotypes Diplotypes
Online Access:	http://link.springer.com/article/10.1186/s13059-019-1709-0

id	doaj-c9258fdd94314d80b31bd0c99666e958
record_format	Article
spelling	doaj-c9258fdd94314d80b31bd0c99666e9582020-11-25T03:31:23ZengBMCGenome Biology1474-760X2019-06-0120111610.1186/s13059-019-1709-0Haplotype-aware diplotyping from noisy long readsJana Ebler0Marina Haukness1Trevor Pesout2Tobias Marschall3Benedict Paten4Center for Bioinformatics, Saarland UniversityUC Santa Cruz Genomics Institute, University of California Santa CruzUC Santa Cruz Genomics Institute, University of California Santa CruzCenter for Bioinformatics, Saarland UniversityUC Santa Cruz Genomics Institute, University of California Santa CruzAbstract Current genotyping approaches for single-nucleotide variations rely on short, accurate reads from second-generation sequencing devices. Presently, third-generation sequencing platforms are rapidly becoming more widespread, yet approaches for leveraging their long but error-prone reads for genotyping are lacking. Here, we introduce a novel statistical framework for the joint inference of haplotypes and genotypes from noisy long reads, which we term diplotyping. Our technique takes full advantage of linkage information provided by long reads. We validate hundreds of thousands of candidate variants that have not yet been included in the high-confidence reference set of the Genome-in-a-Bottle effort.http://link.springer.com/article/10.1186/s13059-019-1709-0Computational genomicsLong readsGenotypingPhasingHaplotypesDiplotypes
collection	DOAJ
language	English
format	Article
sources	DOAJ
author	Jana Ebler Marina Haukness Trevor Pesout Tobias Marschall Benedict Paten
spellingShingle	Jana Ebler Marina Haukness Trevor Pesout Tobias Marschall Benedict Paten Haplotype-aware diplotyping from noisy long reads Genome Biology Computational genomics Long reads Genotyping Phasing Haplotypes Diplotypes
author_facet	Jana Ebler Marina Haukness Trevor Pesout Tobias Marschall Benedict Paten
author_sort	Jana Ebler
title	Haplotype-aware diplotyping from noisy long reads
title_short	Haplotype-aware diplotyping from noisy long reads
title_full	Haplotype-aware diplotyping from noisy long reads
title_fullStr	Haplotype-aware diplotyping from noisy long reads
title_full_unstemmed	Haplotype-aware diplotyping from noisy long reads
title_sort	haplotype-aware diplotyping from noisy long reads
publisher	BMC
series	Genome Biology
issn	1474-760X
publishDate	2019-06-01
description	Abstract Current genotyping approaches for single-nucleotide variations rely on short, accurate reads from second-generation sequencing devices. Presently, third-generation sequencing platforms are rapidly becoming more widespread, yet approaches for leveraging their long but error-prone reads for genotyping are lacking. Here, we introduce a novel statistical framework for the joint inference of haplotypes and genotypes from noisy long reads, which we term diplotyping. Our technique takes full advantage of linkage information provided by long reads. We validate hundreds of thousands of candidate variants that have not yet been included in the high-confidence reference set of the Genome-in-a-Bottle effort.
topic	Computational genomics Long reads Genotyping Phasing Haplotypes Diplotypes
url	http://link.springer.com/article/10.1186/s13059-019-1709-0
work_keys_str_mv	AT janaebler haplotypeawarediplotypingfromnoisylongreads AT marinahaukness haplotypeawarediplotypingfromnoisylongreads AT trevorpesout haplotypeawarediplotypingfromnoisylongreads AT tobiasmarschall haplotypeawarediplotypingfromnoisylongreads AT benedictpaten haplotypeawarediplotypingfromnoisylongreads
_version_	1724571919564406784

Haplotype-aware diplotyping from noisy long reads

Similar Items