Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies.
Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies.
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DOI：
10.1038/s41592-022-01440-3
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发表时间：
2022-06
期刊：
影响因子：
48
通讯作者：
Rhie, Arang
中科院分区：
文献类型：
--
作者：
Cartney, Ann M. Mc;Shafin, Kishwar;Alonge, Michael;Bzikadze, Andrey, V;Formenti, Giulio;Fungtammasan, Arkarachai;Howe, Kerstin;Jain, Chirag;Koren, Sergey;Logsdon, Glennis A.;Miga, Karen H.;Mikheenko, Alla;Paten, Benedict;Shumate, Alaina;Soto, Daniela C.;Sovic, Ivan;Wood, Jonathan Md;Zook, Justin M.;Phillippy, Adam M.;Rhie, Arang
长读长测序技术和基因组组装方法的进步使得最近完成了首次端粒到端粒（T2T）人类基因组组装，解决了复杂的片段重复和大串联重复，包括完整葡萄胎（CHM13）中的着丝粒卫星阵列。尽管源自高度准确的序列，但评估揭示了初始 T2T 装配草案中存在小错误和结构错误的证据。为了纠正这些错误，我们设计了一种新颖的重复感知抛光策略，可以在大重复中进行准确的组装校正，而不会过度校正，最终修复了 51% 的现有错误，并将 PacBio HiFi 和 Illumina k-mers 测量的组装 QV 从 70.2 提高到 73.9。通过将我们的结果与标准自动抛光工具进行比较，我们概述了常见的抛光错误，并为资源有限的基因组项目提供了实用的建议。我们还展示了 HiFi 和 Oxford Nanopore Technologies 读取中的测序偏差如何导致特征组装错误，而这些错误可以通过多种测序技术进行纠正。
Advances in long-read sequencing technologies and genome assembly methods have enabled the recent completion of the first Telomere-to-Telomere (T2T) human genome assembly, which resolves complex segmental duplications and large tandem repeats, including centromeric satellite arrays in a complete hydatidiform mole (CHM13). Though derived from highly accurate sequences, evaluation revealed evidence of small errors and structural misassemblies in the initial T2T draft assembly. To correct these errors, we designed a novel repeat-aware polishing strategy that made accurate assembly corrections in large repeats without overcorrection, ultimately fixing 51% of the existing errors and improving the assembly QV from 70.2 to 73.9 measured from PacBio HiFi and Illumina k-mers. By comparing our results to standard automated polishing tools, we outline common polishing errors and offer practical suggestions for genome projects with limited resources. We also show how sequencing biases in both HiFi and Oxford Nanopore Technologies reads cause signature assembly errors that can be corrected with a diverse panel of sequencing technologies.
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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
影响因子：
48
作者：
Cheng H;Concepcion GT;Feng X;Zhang H;Li H
通讯作者：
Li H
影响因子：
5.8
作者：
Li, Heng
通讯作者：
Li, Heng
DOI：
10.1126/science.abg5289
发表时间：
2021-08-06
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Hufford MB;Seetharam AS;Woodhouse MR;Chougule KM;Ou S;Liu J;Ricci WA;Guo T;Olson A;Qiu Y;Della Coletta R;Tittes S;Hudson AI;Marand AP;Wei S;Lu Z;Wang B;Tello-Ruiz MK;Piri RD;Wang N;Kim DW;Zeng Y;O'Connor CH;Li X;Gilbert AM;Baggs E;Krasileva KV;Portwood JL 2nd;Cannon EKS;Andorf CM;Manchanda N;Snodgrass SJ;Hufnagel DE;Jiang Q;Pedersen S;Syring ML;Kudrna DA;Llaca V;Fengler K;Schmitz RJ;Ross-Ibarra J;Yu J;Gent JI;Hirsch CN;Ware D;Dawe RK
通讯作者：
Dawe RK
影响因子：
5.8
作者：
Li, Heng
通讯作者：
Li, Heng