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nPhase：一种用于多倍体的准确连续相位方法。

nPhase: an accurate and contiguous phasing method for polyploids.

机构信息

Université de Strasbourg, CNRS, GMGM UMR, 7156, Strasbourg, France.

Institut Universitaire de France (IUF), Paris, France.

出版信息

Genome Biol. 2021 Apr 29;22(1):126. doi: 10.1186/s13059-021-02342-x.

DOI:10.1186/s13059-021-02342-x
PMID:33926549
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC8082856/
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.

摘要

虽然基因组测序和组装现在已经很常规，但我们对于多倍体基因组并没有一个完整、精确的认识。现有的多倍体相位分析方法都无法提供准确且连续的单倍型预测。我们开发了 nPhase，这是一种不依赖倍性的工具，它利用长读长和准确的短读长来解决指定倍性样品的基于比对的相位问题（https://github.com/OmarOakheart/nPhase）。nPhase 在模拟和真实多倍体上的测试得到了验证。nPhase 的平均准确率超过 95%，每个单倍型的连续单倍型片段平均达到 1.25 个，覆盖了每个染色体的 90%以上（杂合率≥0.5%）。nPhase 可以用于多倍体的群体基因组学和杂种研究。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/373f/8082856/a1d086178406/13059_2021_2342_Fig11_HTML.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/373f/8082856/121ffbd22ddb/13059_2021_2342_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/373f/8082856/9c5b770e95b0/13059_2021_2342_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/373f/8082856/5693dca3d302/13059_2021_2342_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/373f/8082856/e67d316c4350/13059_2021_2342_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/373f/8082856/6cdbce812994/13059_2021_2342_Fig8_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/373f/8082856/cb0b50de7b7d/13059_2021_2342_Fig9_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/373f/8082856/40852c4a2fac/13059_2021_2342_Fig10_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/373f/8082856/a1d086178406/13059_2021_2342_Fig11_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/373f/8082856/9adb1360dd19/13059_2021_2342_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/373f/8082856/ed405c2c42e9/13059_2021_2342_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/373f/8082856/96ee493ff6ea/13059_2021_2342_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/373f/8082856/121ffbd22ddb/13059_2021_2342_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/373f/8082856/9c5b770e95b0/13059_2021_2342_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/373f/8082856/5693dca3d302/13059_2021_2342_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/373f/8082856/e67d316c4350/13059_2021_2342_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/373f/8082856/6cdbce812994/13059_2021_2342_Fig8_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/373f/8082856/cb0b50de7b7d/13059_2021_2342_Fig9_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/373f/8082856/40852c4a2fac/13059_2021_2342_Fig10_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/373f/8082856/a1d086178406/13059_2021_2342_Fig11_HTML.jpg

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