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NPhase: an accurate and contiguous phasing method for polyploids.

ABSTRACT: While genome sequencing and assembly are now routine, we do not have a full, precise picture of polyploid genomes. No existing polyploid phasing method provides accurate and contiguous haplotype predictions. We developed nPhase, a ploidy agnostic tool that leverages long reads and accurate short reads to solve alignment-based phasing for samples of unspecified ploidy ( https://github.com/OmarOakheart/nPhase ). nPhase is validated by tests on simulated and real polyploids. nPhase obtains on average over 95% accuracy and a contiguous 1.25 haplotigs per haplotype to cover more than 90% of each chromosome (heterozygosity rate ≥ 0.5%). nPhase allows population genomics and hybrid studies of polyploids.

SUBMITTER: Abou Saada O

PROVIDER: S-EPMC8082856 | biostudies-literature | 2021 Apr

REPOSITORIES: biostudies-literature

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nPhase: an accurate and contiguous phasing method for polyploids.

Abou Saada Omar O Tsouris Andreas A Eberlein Chris C Friedrich Anne A Schacherer Joseph J

Genome biology 20210429 1

While genome sequencing and assembly are now routine, we do not have a full, precise picture of polyploid genomes. No existing polyploid phasing method provides accurate and contiguous haplotype predictions. We developed nPhase, a ploidy agnostic tool that leverages long reads and accurate short reads to solve alignment-based phasing for samples of unspecified ploidy ( https://github.com/OmarOakheart/nPhase ). nPhase is validated by tests on simulated and real polyploids. nPhase obtains on avera ...[more]

PMID: 33926549

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