Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data

被引：849

作者：

Carver, Tim ^{[1
]}

Harris, Simon R. ^{[1
]}

Berriman, Matthew ^{[1
]}

Parkhill, Julian ^{[1
]}

McQuillan, Jacqueline A. ^{[1
]}

机构：

[1] Wellcome Trust Sanger Inst, Cambridge CB10 1SA, England

来源：

BIOINFORMATICS | 2012年 / 28卷 / 04期

基金：

英国惠康基金;

关键词：

READ ALIGNMENT; GENOME BROWSER; TRANSCRIPTOME; ANNOTATION; EVOLUTION; PATHOGEN; FORMAT;

D O I：

10.1093/bioinformatics/btr703

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Motivation: High-throughput sequencing (HTS) technologies have made low-cost sequencing of large numbers of samples commonplace. An explosion in the type, not just number, of sequencing experiments has also taken place including genome re-sequencing, population-scale variation detection, whole transcriptome sequencing and genome-wide analysis of protein- bound nucleic acids. Results: We present Artemis as a tool for integrated visualization and computational analysis of different types of HTS datasets in the context of a reference genome and its corresponding annotation.

引用

页码：464 / 469

页数：6

共 40 条

[1] A map of human genome variation from population-scale sequencing [J].

Altshuler, David ;

Durbin, Richard M. ;

Abecasis, Goncalo R. ;

Bentley, David R. ;

Chakravarti, Aravinda ;

Clark, Andrew G. ;

Collins, Francis S. ;

De la Vega, Francisco M. ;

Donnelly, Peter ;

Egholm, Michael ;

Flicek, Paul ;

Gabriel, Stacey B. ;

Gibbs, Richard A. ;

Knoppers, Bartha M. ;

Lander, Eric S. ;

Lehrach, Hans ;

Mardis, Elaine R. ;

McVean, Gil A. ;

Nickerson, DebbieA. ;

Peltonen, Leena ;

Schafer, Alan J. ;

Sherry, Stephen T. ;

Wang, Jun ;

Wilson, Richard K. ;

Gibbs, Richard A. ;

Deiros, David ;

Metzker, Mike ;

Muzny, Donna ;

Reid, Jeff ;

Wheeler, David ;

Wang, Jun ;

Li, Jingxiang ;

Jian, Min ;

Li, Guoqing ;

Li, Ruiqiang ;

Liang, Huiqing ;

Tian, Geng ;

Wang, Bo ;

Wang, Jian ;

Wang, Wei ;

Yang, Huanming ;

Zhang, Xiuqing ;

Zheng, Huisong ;

Lander, Eric S. ;

Altshuler, David L. ;

Ambrogio, Lauren ;

Bloom, Toby ;

Cibulskis, Kristian ;

Fennell, Tim J. ;

Gabriel, Stacey B. .

NATURE, 2010, 467 (7319) :1061-1073

[2] Differential expression analysis for sequence count data [J].

Anders, Simon ;

Huber, Wolfgang .

GENOME BIOLOGY, 2010, 11 (10)

[3] The genome of the blood fluke Schistosoma mansoni [J].

Berriman, Matthew ;

Haas, Brian J. ;

LoVerde, Philip T. ;

Wilson, R. Alan ;

Dillon, Gary P. ;

Cerqueira, Gustavo C. ;

Mashiyama, Susan T. ;

Al-Lazikani, Bissan ;

Andrade, Luiza F. ;

Ashton, Peter D. ;

Aslett, Martin A. ;

Bartholomeu, Daniella C. ;

Blandin, Gaelle ;

Caffrey, Conor R. ;

Coghlan, Avril ;

Coulson, Richard ;

Day, Tim A. ;

Delcher, Art ;

DeMarco, Ricardo ;

Djikeng, Appolinaire ;

Eyre, Tina ;

Gamble, John A. ;

Ghedin, Elodie ;

Gu, Yong ;

Hertz-Fowler, Christiane ;

Hirai, Hirohisha ;

Hirai, Yuriko ;

Houston, Robin ;

Ivens, Alasdair ;

Johnston, David A. ;

Lacerda, Daniela ;

Macedo, Camila D. ;

McVeigh, Paul ;

Ning, Zemin ;

Oliveira, Guilherme ;

Overington, John P. ;

Parkhill, Julian ;

Pertea, Mihaela ;

Pierce, Raymond J. ;

Protasio, Anna V. ;

Quail, Michael A. ;

Rajandream, Marie-Adele ;

Rogers, Jane ;

Sajid, Mohammed ;

Salzberg, Steven L. ;

Stanke, Mario ;

Tivey, Adrian R. ;

White, Owen ;

Williams, David L. ;

Wortman, Jennifer .

NATURE, 2009, 460 (7253) :352-U65

[4] Comprehensive annotation of the transcriptome of the human fungal pathogen Candida albicans using RNA-seq [J].

Bruno, Vincent M. ;

Wang, Zhong ;

Marjani, Sadie L. ;

Euskirchen, Ghia M. ;

Martin, Jeffrey ;

Sherlock, Gavin ;

Snyder, Michael .

GENOME RESEARCH, 2010, 20 (10) :1451-1458

[5] BamView: viewing mapped read alignment data in the context of the reference sequence [J].

Carver, Tim ;

Bohme, Ulrike ;

Otto, Thomas D. ;

Parkhill, Julian ;

Berriman, Matthew .

BIOINFORMATICS, 2010, 26 (05) :676-677

[6] ACT: the Artemis comparison tool [J].

Carver, TJ ;

Rutherford, KM ;

Berriman, M ;

Rajandream, MA ;

Barrell, BG ;

Parkhill, J .

BIOINFORMATICS, 2005, 21 (16) :3422-3423

[7] Rapid Pneumococcal Evolution in Response to Clinical Interventions [J].

Croucher, Nicholas J. ;

Harris, Simon R. ;

Fraser, Christophe ;

Quail, Michael A. ;

Burton, John ;

van der Linden, Mark ;

McGee, Lesley ;

von Gottberg, Anne ;

Song, Jae Hoon ;

Ko, Kwan Soo ;

Pichon, Bruno ;

Baker, Stephen ;

Parry, Christopher M. ;

Lambertsen, Lotte M. ;

Shahinas, Dea ;

Pillai, Dylan R. ;

Mitchell, Timothy J. ;

Dougan, Gordon ;

Tomasz, Alexander ;

Klugman, Keith P. ;

Parkhill, Julian ;

Hanage, William P. ;

Bentley, Stephen D. .

SCIENCE, 2011, 331 (6016) :430-434

[8] Studying bacterial transcriptomes using RNA-seq [J].

Croucher, Nicholas J. ;

Thomson, Nicholas R. .

CURRENT OPINION IN MICROBIOLOGY, 2010, 13 (05) :619-624

[9] The variant call format and VCFtools [J].

Danecek, Petr ;

Auton, Adam ;

Abecasis, Goncalo ;

Albers, Cornelis A. ;

Banks, Eric ;

DePristo, Mark A. ;

Handsaker, Robert E. ;

Lunter, Gerton ;

Marth, Gabor T. ;

Sherry, Stephen T. ;

McVean, Gilean ;

Durbin, Richard .

BIOINFORMATICS, 2011, 27 (15) :2156-2158

[10] The Drosophila melanogaster transcriptome by paired-end RNA sequencing [J].

Daines, Bryce ;

Wang, Hui ;

Wang, Liguo ;

Li, Yumei ;

Han, Yi ;

Emmert, David ;

Gelbart, William ;

Wang, Xia ;

Li, Wei ;

Gibbs, Richard ;

Chen, Rui .

GENOME RESEARCH, 2011, 21 (02) :315-324

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