Solving the problem of comparing whole bacterial genomes across different sequencing platforms.
Solving the problem of comparing whole bacterial genomes across different sequencing platforms.
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DOI：
10.1371/journal.pone.0104984
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发表时间：
2014
期刊：
影响因子：
3.7
通讯作者：
Lund O
中科院分区：
文献类型：
--
作者：
Kaas RS;Leekitcharoenphon P;Aarestrup FM;Lund O
全基因组测序（WGS）在传染病暴发的实时监测和识别方面显示出巨大的潜力。然而，对多个实验室使用多种技术生成的数据进行快速可靠的比较至关重要。到目前为止，研究都集中在使用一种技术，因为每种技术都有系统性的偏差，使得从不同平台生成的数据难以整合。我们开发了两种不同的程序，用于在多个平台上识别WGS数据中的可变位点和推断遗传。在三个细菌数据集上评估所述方法，并在三个不同的平台（Illumina，454，Ion Torrent）上测序。我们表明，该方法能够克服测序仪引起的系统偏差，并推断出预期的同源性。可以得出结论，这些新程序成功的原因是由于验证了分析中包含的所有信息网站。这些程序以网络工具的形式提供。
Whole genome sequencing (WGS) shows great potential for real-time monitoring and identification of infectious disease outbreaks. However, rapid and reliable comparison of data generated in multiple laboratories and using multiple technologies is essential. So far studies have focused on using one technology because each technology has a systematic bias making integration of data generated from different platforms difficult. We developed two different procedures for identifying variable sites and inferring phylogenies in WGS data across multiple platforms. The methods were evaluated on three bacterial data sets and sequenced on three different platforms (Illumina, 454, Ion Torrent). We show that the methods are able to overcome the systematic biases caused by the sequencers and infer the expected phylogenies. It is concluded that the cause of the success of these new procedures is due to a validation of all informative sites that are included in the analysis. The procedures are available as web tools.
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影响因子：
4.4
作者：
Leekitcharoenphon P;Kaas RS;Thomsen MC;Friis C;Rasmussen S;Aarestrup FM
通讯作者：
Aarestrup FM
影响因子：
6.4
作者：
Price LB;Stegger M;Hasman H;Aziz M;Larsen J;Andersen PS;Pearson T;Waters AE;Foster JT;Schupp J;Gillece J;Driebe E;Liu CM;Springer B;Zdovc I;Battisti A;Franco A;Zmudzki J;Schwarz S;Butaye P;Jouy E;Pomba C;Porrero MC;Ruimy R;Smith TC;Robinson DA;Weese JS;Arriola CS;Yu F;Laurent F;Keim P;Skov R;Aarestrup FM
通讯作者：
Aarestrup FM
DOI：
10.1093/bioinformatics/btq033
发表时间：
2010-03-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Quinlan AR;Hall IM
通讯作者：
Hall IM
影响因子：
11.8
作者：
Aarestrup FM;Brown EW;Detter C;Gerner-Smidt P;Gilmour MW;Harmsen D;Hendriksen RS;Hewson R;Heymann DL;Johansson K;Ijaz K;Keim PS;Koopmans M;Kroneman A;Lo Fo Wong D;Lund O;Palm D;Sawanpanyalert P;Sobel J;Schlundt J
通讯作者：
Schlundt J
影响因子：
9.4
作者：
Joensen, Katrine Grimstrup;Scheutz, Flemming;Aarestrup, Frank M.
通讯作者：
Aarestrup, Frank M.