Haplotype-aware variant calling with PEPPER-Margin-DeepVariant enables high accuracy in nanopore long-reads.
Haplotype-aware variant calling with PEPPER-Margin-DeepVariant enables high accuracy in nanopore long-reads.
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DOI：
10.1038/s41592-021-01299-w
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发表时间：
2021-11
期刊：
影响因子：
48
通讯作者：
Paten B
中科院分区：
文献类型：
--
作者：
Shafin K;Pesout T;Chang PC;Nattestad M;Kolesnikov A;Goel S;Baid G;Kolmogorov M;Eizenga JM;Miga KH;Carnevali P;Jain M;Carroll A;Paten B
长读段测序具有通过到达目前难以映射的区域并常规地将相邻变异连接在一起以实现基于读段的定相来改变变异检测的潜力。第三代纳米孔序列数据已显示出较长的读取长度，但其新型基于孔的信号的当前解释方法具有独特的误差分布，使得准确分析具有挑战性。在这里，我们介绍了一个单倍型感知的变体调用管道PEPPER-Margin-DeepVariant，它使用纳米孔数据产生最先进的变体调用结果。我们表明，我们的基于纳米孔的方法在整个基因组规模上优于基于短读段的单核苷酸变体鉴定方法，并在基于短读段的基因分型失败的片段重复和低映射性区域中产生高质量的单核苷酸变体。我们表明，我们的流水线可以在基因组中提供高度连续的相位块，其中纳米孔读数连续跨越六个样品中85%至92%的注释基因。我们还将PEPPER-Margin-DeepVariant扩展到PacBio HiFi数据，提供了一个比当前WhatsHap-DeepVariant标准具有上级性能的高效解决方案。最后，我们展示了从头组装抛光方法，该方法使用纳米孔和PacBio HiFi读取来产生具有高精度的二倍体组装（Q35+纳米孔抛光和Q40+ PacBio-HiFi抛光）。关于研究设计的进一步信息可在与本文链接的《自然研究报告摘要》中找到。
Long-read sequencing has the potential to transform variant detection by reaching currently difficult-to-map regions and routinely linking together adjacent variations to enable read based phasing. Third-generation nanopore sequence data has demonstrated a long read length, but current interpretation methods for its novel pore-based signal have unique error profiles, making accurate analysis challenging. Here, we introduce a haplotype-aware variant calling pipeline PEPPER-Margin-DeepVariant that produces state-of-the-art variant calling results with nanopore data. We show that our nanopore-based method outperforms the short-read-based single nucleotide variant identification method at the whole genome-scale and produces high quality single nucleotide variants in segmental duplications and low-mappability regions where short-read based genotyping fails. We show that our pipeline can provide highly-contiguous phase blocks across the genome with nanopore reads, contiguously spanning between 85% to 92% of annotated genes across six samples. We also extend PEPPER-Margin-DeepVariant to PacBio HiFi data, providing an efficient solution with superior performance than the current WhatsHap-DeepVariant standard. Finally, we demonstrate de novo assembly polishing methods that use nanopore and PacBio HiFi reads to produce diploid assemblies with high accuracy (Q35+ nanopore-polished and Q40+ PacBio-HiFi-polished). Further information on research design is available in the Nature Research Reporting Summary linked to this article.
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影响因子：
46.9
作者：
Jain M;Olsen HE;Turner DJ;Stoddart D;Bulazel KV;Paten B;Haussler D;Willard HF;Akeson M;Miga KH
通讯作者：
Miga KH
影响因子：
7
作者：
Huddleston J;Chaisson MJP;Steinberg KM;Warren W;Hoekzema K;Gordon D;Graves-Lindsay TA;Munson KM;Kronenberg ZN;Vives L;Peluso P;Boitano M;Chin CS;Korlach J;Wilson RK;Eichler EE
通讯作者：
Eichler EE
来自1,092个人基因组的遗传变异的综合图。
影响因子：
64.8
作者：
通讯作者：
--
影响因子：
7
作者：
Harrow J;Frankish A;Gonzalez JM;Tapanari E;Diekhans M;Kokocinski F;Aken BL;Barrell D;Zadissa A;Searle S;Barnes I;Bignell A;Boychenko V;Hunt T;Kay M;Mukherjee G;Rajan J;Despacio-Reyes G;Saunders G;Steward C;Harte R;Lin M;Howald C;Tanzer A;Derrien T;Chrast J;Walters N;Balasubramanian S;Pei B;Tress M;Rodriguez JM;Ezkurdia I;van Baren J;Brent M;Haussler D;Kellis M;Valencia A;Reymond A;Gerstein M;Guigó R;Hubbard TJ
通讯作者：
Hubbard TJ
影响因子：
14.9
作者：
Frankish A;Diekhans M;Ferreira AM;Johnson R;Jungreis I;Loveland J;Mudge JM;Sisu C;Wright J;Armstrong J;Barnes I;Berry A;Bignell A;Carbonell Sala S;Chrast J;Cunningham F;Di Domenico T;Donaldson S;Fiddes IT;García Girón C;Gonzalez JM;Grego T;Hardy M;Hourlier T;Hunt T;Izuogu OG;Lagarde J;Martin FJ;Martínez L;Mohanan S;Muir P;Navarro FCP;Parker A;Pei B;Pozo F;Ruffier M;Schmitt BM;Stapleton E;Suner MM;Sycheva I;Uszczynska-Ratajczak B;Xu J;Yates A;Zerbino D;Zhang Y;Aken B;Choudhary JS;Gerstein M;Guigó R;Hubbard TJP;Kellis M;Paten B;Reymond A;Tress ML;Flicek P
通讯作者：
Flicek P