A field guide to whole-genome sequencing, assembly and annotation.
A field guide to whole-genome sequencing, assembly and annotation.
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DOI：
10.1111/eva.12178
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发表时间：
2014-11
影响因子：
4.1
通讯作者：
Wolf JB
中科院分区：
文献类型：
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作者：
Ekblom R;Wolf JB
基因组测序项目长期以来局限于生物医学模式生物，且需要大型联盟的协同努力。高通量测序技术的快速进步以及生物信息学工具的同步发展使该领域大众化。现在，生态进化和保护领域的单个研究小组也能够为所选的任何生物生成从头组装的基因组草图序列。由于此类工作涉及成本和大量精力，重要的第一步是彻底考虑基因组序列对于解决手头的生物学问题是否必要。一旦做出这个决定，一个基因组项目就需要针对所涉及的生物以及基因组草图的预期质量进行精心规划。在此，我们简要回顾该领域的技术现状，并逐步介绍基因组测序、组装和注释所涉及的工作流程，尤其针对大型和复杂的基因组。本教程面向具有保护遗传学背景的科学家，但更广泛地说，它为从事全基因组测序项目的研究人员提供了有用的实践指导。
Genome sequencing projects were long confined to biomedical model organisms and required the concerted effort of large consortia. Rapid progress in high-throughput sequencing technology and the simultaneous development of bioinformatic tools have democratized the field. It is now within reach for individual research groups in the eco-evolutionary and conservation community to generate de novo draft genome sequences for any organism of choice. Because of the cost and considerable effort involved in such an endeavour, the important first step is to thoroughly consider whether a genome sequence is necessary for addressing the biological question at hand. Once this decision is taken, a genome project requires careful planning with respect to the organism involved and the intended quality of the genome draft. Here, we briefly review the state of the art within this field and provide a step-by-step introduction to the workflow involved in genome sequencing, assembly and annotation with particular reference to large and complex genomes. This tutorial is targeted at scientists with a background in conservation genetics, but more generally, provides useful practical guidance for researchers engaging in whole-genome sequencing projects.
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DOI：
10.1073/pnas.1314090110
发表时间：
2013-09-03
影响因子：
11.1
作者：
Chu, Te-Chin;Lu, Chen-Hua;Shih, Arthur Chun-Chieh
通讯作者：
Shih, Arthur Chun-Chieh
影响因子：
64.8
作者：
通讯作者：
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影响因子：
64.8
作者：
Dasmahapatra, Kanchon K.;Walters, James R.;Briscoe, Adriana D.;Davey, John W.;Whibley, Annabel;Nadeau, Nicola J.;Zimin, Aleksey V.;Hughes, Daniel S. T.;Ferguson, Laura C.;Martin, Simon H.;Salazar, Camilo;Lewis, James J.;Adler, Sebastian;Ahn, Seung-Joon;Baker, Dean A.;Baxter, Simon W.;Chamberlain, Nicola L.;Chauhan, Ritika;Counterman, Brian A.;Dalmay, Tamas;Gilbert, Lawrence E.;Gordon, Karl;Heckel, David G.;Hines, Heather M.;Hoff, Katharina J.;Holland, Peter W. H.;Jacquin-Joly, Emmanuelle;Jiggins, Francis M.;Jones, Robert T.;Kapan, Durrell D.;Kersey, Paul;Lamas, Gerardo;Lawson, Daniel;Mapleson, Daniel;Maroja, Luana S.;Martin, Arnaud;Moxon, Simon;Palmer, William J.;Papa, Riccardo;Papanicolaou, Alexie;Pauchet, Yannick;Ray, David A.;Rosser, Neil;Salzberg, Steven L.;Supple, Megan A.;Surridge, Alison;Tenger-Trolander, Ayse;Vogel, Heiko;Wilkinson, Paul A.;Wilson, Derek;Yorke, James A.;Yuan, Furong;Balmuth, Alexi L.;Eland, Cathlene;Gharbi, Karim;Thomson, Marian;Gibbs, Richard A.;Han, Yi;Jayaseelan, Joy C.;Kovar, Christie;Mathew, Tittu;Muzny, Donna M.;Ongeri, Fiona;Pu, Ling-Ling;Qu, Jiaxin;Thornton, Rebecca L.;Worley, Kim C.;Wu, Yuan-Qing;Linares, Mauricio;Blaxter, Mark L.;Ffrench-Constant, Richard H.;Joron, Mathieu;Kronforst, Marcus R.;Mullen, Sean P.;Reed, Robert D.;Scherer, Steven E.;Richards, Stephen;Mallet, James;McMillan, W. Owen;Jiggins, Chris D.
通讯作者：
Jiggins, Chris D.
影响因子：
1.7
作者：
Boisvert, Sebastien;Laviolette, Francois;Corbeil, Jacques
通讯作者：
Corbeil, Jacques
使用下一代 DNA 测序数据进行变异发现和基因分型的框架。
影响因子：
30.8
作者：
通讯作者：
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