A survey of tools for variant analysis of next-generation genome sequencing data.
A survey of tools for variant analysis of next-generation genome sequencing data.
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DOI：
10.1093/bib/bbs086
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发表时间：
2014-03
影响因子：
9.5
通讯作者：
Trajanoski Z
中科院分区：
文献类型：
--
作者：
Pabinger S;Dander A;Fischer M;Snajder R;Sperk M;Efremova M;Krabichler B;Speicher MR;Zschocke J;Trajanoski Z
基因组测序技术的最新进展为表征个体基因组景观和识别与诊断和治疗相关的突变提供了前所未有的机会。具体而言，使用下一代测序（NGS）技术的全外显子组测序由于成本适中、可管理的数据量和对分析结果的直接解释而在人类遗传学界越来越受欢迎。虽然全外显子组和在不久的将来全基因组测序正在成为商品，但数据分析仍然带来了重大挑战，并导致开发了大量支持分析工作流程特定部分或提供完整解决方案的工具。在这里，我们调查了205种用于全基因组/全外显子组测序数据分析的工具，支持五个不同的分析步骤：质量评估，比对，变异识别，变异注释和可视化。我们报告了各个工具的功能、特性和具体要求的概述。然后，我们选择了32个程序进行变异识别，变异注释和可视化，使用四个数据集进行实际评估：一组来自患有罕见疾病的两名患者的外显子组数据，用于测试种系突变的鉴定，两组癌症数据，用于测试体细胞突变、拷贝数变异和结构变异的变异呼叫者，和一个用于测试拷贝数变异的鉴定的半合成数据集。我们对NGS工具的全面调查和评估为研究孟德尔疾病、复杂疾病和癌症的人类遗传学家提供了有价值的指导。
Recent advances in genome sequencing technologies provide unprecedented opportunities to characterize individual genomic landscapes and identify mutations relevant for diagnosis and therapy. Specifically, whole-exome sequencing using next-generation sequencing (NGS) technologies is gaining popularity in the human genetics community due to the moderate costs, manageable data amounts and straightforward interpretation of analysis results. While whole-exome and, in the near future, whole-genome sequencing are becoming commodities, data analysis still poses significant challenges and led to the development of a plethora of tools supporting specific parts of the analysis workflow or providing a complete solution. Here, we surveyed 205 tools for whole-genome/whole-exome sequencing data analysis supporting five distinct analytical steps: quality assessment, alignment, variant identification, variant annotation and visualization. We report an overview of the functionality, features and specific requirements of the individual tools. We then selected 32 programs for variant identification, variant annotation and visualization, which were subjected to hands-on evaluation using four data sets: one set of exome data from two patients with a rare disease for testing identification of germline mutations, two cancer data sets for testing variant callers for somatic mutations, copy number variations and structural variations, and one semi-synthetic data set for testing identification of copy number variations. Our comprehensive survey and evaluation of NGS tools provides a valuable guideline for human geneticists working on Mendelian disorders, complex diseases and cancers.
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DOI：
10.1093/bioinformatics/btr612
发表时间：
2012-01-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Asmann YW;Middha S;Hossain A;Baheti S;Li Y;Chai HS;Sun Z;Duffy PH;Hadad AA;Nair A;Liu X;Zhang Y;Klee EW;Kalari KR;Kocher JP
通讯作者：
Kocher JP
影响因子：
30.8
作者：
Alkan, Can;Kidd, Jeffrey M.;Marques-Bonet, Tomas;Aksay, Gozde;Antonacci, Francesca;Hormozdiari, Fereydoun;Kitzman, Jacob O.;Baker, Carl;Malig, Maika;Mutlu, Onur;Sahinalp, S. Cenk;Gibbs, Richard A.;Eichler, Evan E.
通讯作者：
Eichler, Evan E.
影响因子：
9.5
作者：
Carver, Tim;Harris, Simon R.;McQuillan, Jacqueline A.
通讯作者：
McQuillan, Jacqueline A.
影响因子：
64.8
作者：
Boyden, Lynn M.;Choi, Murim;Choate, Keith A.;Nelson-Williams, Carol J.;Farhi, Anita;Toka, Hakan R.;Tikhonova, Irina R.;Bjornson, Robert;Mane, Shrikant M.;Colussi, Giacomo;Lebel, Marcel;Gordon, Richard D.;Semmekrot, Ben A.;Poujol, Alain;Valimaki, Matti J.;De Ferrari, Maria E.;Sanjad, Sami A.;Gutkin, Michael;Karet, Fiona E.;Tucci, Joseph R.;Stockigt, Jim R.;Keppler-Noreuil, Kim M.;Porter, Craig C.;Anand, Sudhir K.;Whiteford, Margo L.;Davis, Ira D.;Dewar, Stephanie B.;Bettinelli, Alberto;Fadrowski, Jeffrey J.;Belsha, Craig W.;Hunley, Tracy E.;Nelson, Raoul D.;Trachtman, Howard;Cole, Trevor R. P.;Pinsk, Maury;Bockenhauer, Detlef;Shenoy, Mohan;Vaidyanathan, Priya;Foreman, John W.;Rasoulpour, Majid;Thameem, Farook;Al-Shahrouri, Hania Z.;Radhakrishnan, Jai;Gharavi, Ali G.;Goilav, Beatrice;Lifton, Richard P.
通讯作者：
Lifton, Richard P.
影响因子：
64.8
作者：
Berger, Michael F.;Lawrence, Michael S.;Demichelis, Francesca;Drier, Yotam;Cibulskis, Kristian;Sivachenko, Andrey Y.;Sboner, Andrea;Esgueva, Raquel;Pflueger, Dorothee;Sougnez, Carrie;Onofrio, Robert;Carter, Scott L.;Park, Kyung;Habegger, Lukas;Ambrogio, Lauren;Fennell, Timothy;Parkin, Melissa;Saksena, Gordon;Voet, Douglas;Ramos, Alex H.;Pugh, Trevor J.;Wilkinson, Jane;Fisher, Sheila;Winckler, Wendy;Mahan, Scott;Ardlie, Kristin;Baldwin, Jennifer;Simons, Jonathan W.;Kitabayashi, Naoki;MacDonald, Theresa Y.;Kantoff, Philip W.;Chin, Lynda;Gabriel, Stacey B.;Gerstein, Mark B.;Golub, Todd R.;Meyerson, Matthew;Tewari, Ashutosh;Lander, Eric S.;Getz, Gad;Rubin, Mark A.;Garraway, Levi A.
通讯作者：
Garraway, Levi A.