Swift: primary data analysis for the Illumina Solexa sequencing platform.
Swift: primary data analysis for the Illumina Solexa sequencing platform.
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DOI：
10.1093/bioinformatics/btp383
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发表时间：
2009-09-01
期刊：
影响因子：
--
通讯作者：
Brown C
中科院分区：
文献类型：
--
作者：
Whiteford N;Skelly T;Curtis C;Ritchie ME;Löhr A;Zaranek AW;Abnizova I;Brown C
动机：原始数据分析方法在第二代DNA测序中至关重要。改进的方法有可能提高收率和降低错误率。公开记录的分析工具使用户能够理解主要数据，这对于他们的科学工作的优化和有效性非常重要。在这篇文章中，我们描述了Swift，一个在Illumina Solexa测序平台上执行初级数据分析的新工具。Swift是在供应商自己的软件之外的第一个工具，它完成了从原始图像到基本通话的完整分析过程。因此，它提供了供应商提供的工具的替代方案和独立验证。我们的研究结果表明，在错误率相当的情况下，Swift能够将产量提高13.8%。可用性和实现：Swift在c++中实现，在Linux下支持。它是在开放源代码许可（LGPL3）下提供的，允许研究人员在平台上进行构建。Swift可从http://swiftng.sourceforge.net获得。联系:new@sgenomics.org;nava.whiteford@nanoporetech.com补充信息：补充数据可在Bioinformatics网站在线获得。
Motivation: Primary data analysis methods are of critical importance in second generation DNA sequencing. Improved methods have the potential to increase yield and reduce the error rates. Openly documented analysis tools enable the user to understand the primary data, this is important for the optimization and validity of their scientific work. Results: In this article, we describe Swift, a new tool for performing primary data analysis on the Illumina Solexa Sequencing Platform. Swift is the first tool, outside of the vendors own software, which completes the full analysis process, from raw images through to base calls. As such it provides an alternative to, and independent validation of, the vendor supplied tool. Our results show that Swift is able to increase yield by 13.8%, at comparable error rate. Availability and Implementation: Swift is implemented in C++and supported under Linux. It is supplied under an open source license (LGPL3), allowing researchers to build upon the platform. Swift is available from http://swiftng.sourceforge.net. Contact: new@sgenomics.org; nava.whiteford@nanoporetech.com Supplementary information: Supplementary data are available at Bioinformatics online.
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影响因子：
12.3
作者：
Lin S;Carvalho B;Cutler DJ;Arking DE;Chakravarti A;Irizarry RA
通讯作者：
Irizarry RA
影响因子：
5.8
作者：
Cope, LM;Irizarry, RA;Speed, TP
通讯作者：
Speed, TP
影响因子：
3
作者：
Rougemont, Jacques;Amzallag, Arnaud;Naef, Felix
通讯作者：
Naef, Felix
影响因子：
64.8
作者：
Bentley DR;Balasubramanian S;Swerdlow HP;Smith GP;Milton J;Brown CG;Hall KP;Evers DJ;Barnes CL;Bignell HR;Boutell JM;Bryant J;Carter RJ;Keira Cheetham R;Cox AJ;Ellis DJ;Flatbush MR;Gormley NA;Humphray SJ;Irving LJ;Karbelashvili MS;Kirk SM;Li H;Liu X;Maisinger KS;Murray LJ;Obradovic B;Ost T;Parkinson ML;Pratt MR;Rasolonjatovo IM;Reed MT;Rigatti R;Rodighiero C;Ross MT;Sabot A;Sankar SV;Scally A;Schroth GP;Smith ME;Smith VP;Spiridou A;Torrance PE;Tzonev SS;Vermaas EH;Walter K;Wu X;Zhang L;Alam MD;Anastasi C;Aniebo IC;Bailey DM;Bancarz IR;Banerjee S;Barbour SG;Baybayan PA;Benoit VA;Benson KF;Bevis C;Black PJ;Boodhun A;Brennan JS;Bridgham JA;Brown RC;Brown AA;Buermann DH;Bundu AA;Burrows JC;Carter NP;Castillo N;Chiara E Catenazzi M;Chang S;Neil Cooley R;Crake NR;Dada OO;Diakoumakos KD;Dominguez-Fernandez B;Earnshaw DJ;Egbujor UC;Elmore DW;Etchin SS;Ewan MR;Fedurco M;Fraser LJ;Fuentes Fajardo KV;Scott Furey W;George D;Gietzen KJ;Goddard CP;Golda GS;Granieri PA;Green DE;Gustafson DL;Hansen NF;Harnish K;Haudenschild CD;Heyer NI;Hims MM;Ho JT;Horgan AM;Hoschler K;Hurwitz S;Ivanov DV;Johnson MQ;James T;Huw Jones TA;Kang GD;Kerelska TH;Kersey AD;Khrebtukova I;Kindwall AP;Kingsbury Z;Kokko-Gonzales PI;Kumar A;Laurent MA;Lawley CT;Lee SE;Lee X;Liao AK;Loch JA;Lok M;Luo S;Mammen RM;Martin JW;McCauley PG;McNitt P;Mehta P;Moon KW;Mullens JW;Newington T;Ning Z;Ling Ng B;Novo SM;O'Neill MJ;Osborne MA;Osnowski A;Ostadan O;Paraschos LL;Pickering L;Pike AC;Pike AC;Chris Pinkard D;Pliskin DP;Podhasky J;Quijano VJ;Raczy C;Rae VH;Rawlings SR;Chiva Rodriguez A;Roe PM;Rogers J;Rogert Bacigalupo MC;Romanov N;Romieu A;Roth RK;Rourke NJ;Ruediger ST;Rusman E;Sanches-Kuiper RM;Schenker MR;Seoane JM;Shaw RJ;Shiver MK;Short SW;Sizto NL;Sluis JP;Smith MA;Ernest Sohna Sohna J;Spence EJ;Stevens K;Sutton N;Szajkowski L;Tregidgo CL;Turcatti G;Vandevondele S;Verhovsky Y;Virk SM;Wakelin S;Walcott GC;Wang J;Worsley GJ;Yan J;Yau L;Zuerlein M;Rogers J;Mullikin JC;Hurles ME;McCooke NJ;West JS;Oaks FL;Lundberg PL;Klenerman D;Durbin R;Smith AJ
通讯作者：
Smith AJ
影响因子：
5.8
作者：
Ritchie, Matthew E.;Silver, Jeremy;Smyth, Gordon K.
通讯作者：
Smyth, Gordon K.