Comparative Annotation Toolkit (CAT)-simultaneous clade and personal genome annotation.
Comparative Annotation Toolkit (CAT)-simultaneous clade and personal genome annotation.
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DOI：
10.1101/gr.233460.117
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发表时间：
2018-07
期刊：
影响因子：
7
通讯作者：
Paten B
中科院分区：
文献类型：
--
作者：
Fiddes IT;Armstrong J;Diekhans M;Nachtweide S;Kronenberg ZN;Underwood JG;Gordon D;Earl D;Keane T;Eichler EE;Haussler D;Stanke M;Paten B
最近引入的低成本、长读段和读段云测序技术，加上开发高效算法的巨大努力，使得负担得起的、高质量的从头序列组装成为一个现实的命题。其结果是新的、超连续的基因组组装的爆炸式增长。为了比较这些基因组，我们需要强大的基因组注释方法。我们描述了完全开源的比较注释工具包（CAT），它提供了一种灵活的方式，同时注释整个分支和确定正字法的关系。我们表明，CAT可用于改善大鼠基因组的注释，注释类人猿，注释一组不同的哺乳动物，并注释个人，二倍体人类基因组。我们展示了由此发现的新基因，异构体和结构变异，即使在基因组以及研究大鼠和大猩猩，以及如何这些注释提高跨物种的RNA表达实验。
The recent introductions of low-cost, long-read, and read-cloud sequencing technologies coupled with intense efforts to develop efficient algorithms have made affordable, high-quality de novo sequence assembly a realistic proposition. The result is an explosion of new, ultracontiguous genome assemblies. To compare these genomes, we need robust methods for genome annotation. We describe the fully open source Comparative Annotation Toolkit (CAT), which provides a flexible way to simultaneously annotate entire clades and identify orthology relationships. We show that CAT can be used to improve annotations on the rat genome, annotate the great apes, annotate a diverse set of mammals, and annotate personal, diploid human genomes. We demonstrate the resulting discovery of novel genes, isoforms, and structural variants—even in genomes as well studied as rat and the great apes—and how these annotations improve cross-species RNA expression experiments.
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影响因子：
5.8
作者：
Hickey, Glenn;Paten, Benedict;Haussler, David
通讯作者：
Haussler, David
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
DOI：
10.1126/science.1253451
发表时间：
2014-12-12
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Jarvis ED;Mirarab S;Aberer AJ;Li B;Houde P;Li C;Ho SY;Faircloth BC;Nabholz B;Howard JT;Suh A;Weber CC;da Fonseca RR;Li J;Zhang F;Li H;Zhou L;Narula N;Liu L;Ganapathy G;Boussau B;Bayzid MS;Zavidovych V;Subramanian S;Gabaldón T;Capella-Gutiérrez S;Huerta-Cepas J;Rekepalli B;Munch K;Schierup M;Lindow B;Warren WC;Ray D;Green RE;Bruford MW;Zhan X;Dixon A;Li S;Li N;Huang Y;Derryberry EP;Bertelsen MF;Sheldon FH;Brumfield RT;Mello CV;Lovell PV;Wirthlin M;Schneider MP;Prosdocimi F;Samaniego JA;Vargas Velazquez AM;Alfaro-Núñez A;Campos PF;Petersen B;Sicheritz-Ponten T;Pas A;Bailey T;Scofield P;Bunce M;Lambert DM;Zhou Q;Perelman P;Driskell AC;Shapiro B;Xiong Z;Zeng Y;Liu S;Li Z;Liu B;Wu K;Xiao J;Yinqi X;Zheng Q;Zhang Y;Yang H;Wang J;Smeds L;Rheindt FE;Braun M;Fjeldsa J;Orlando L;Barker FK;Jønsson KA;Johnson W;Koepfli KP;O'Brien S;Haussler D;Ryder OA;Rahbek C;Willerslev E;Graves GR;Glenn TC;McCormack J;Burt D;Ellegren H;Alström P;Edwards SV;Stamatakis A;Mindell DP;Cracraft J;Braun EL;Warnow T;Jun W;Gilbert MT;Zhang G
通讯作者：
Zhang G
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
DOI：
10.1126/science.aae0344
发表时间：
2016-04-01
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Gordon D;Huddleston J;Chaisson MJ;Hill CM;Kronenberg ZN;Munson KM;Malig M;Raja A;Fiddes I;Hillier LW;Dunn C;Baker C;Armstrong J;Diekhans M;Paten B;Shendure J;Wilson RK;Haussler D;Chin CS;Eichler EE
通讯作者：
Eichler EE