ToTem: a tool for variant calling pipeline optimization.
ToTem: a tool for variant calling pipeline optimization.
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DOI：
10.1186/s12859-018-2227-x
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发表时间：
2018-06-26
影响因子：
3
通讯作者：
Pospisilova S
中科院分区：
文献类型：
--
作者：
Tom N;Tom O;Malcikova J;Pavlova S;Kubesova B;Rausch T;Kolarik M;Benes V;Bystry V;Pospisilova S
下一代测序（NGS）数据的高通量生物信息学分析通常需要具有挑战性的管道优化。关键问题是选择合适的工具和参数以达到最佳的查准率和查全率。这里我们介绍ToTem，一个自动化管道优化工具。ToTem是一个独立的web应用程序，具有全面的图形用户界面（GUI）。ToTem是用Java和PHP编写的，底层连接到MySQL数据库。它的主要作用是自动生成、执行和基准测试不同的变体调用管道设置。我们的工具允许从过程的任何级别开始分析，并且可以插入几乎任何工具或代码。为了防止管道参数的过度拟合，ToTem通过使用交叉验证技术来确保这些参数的可重复性，该技术会惩罚最终的精度、召回率和F-measure。结果被解释为交互式图形和表格，允许根据用户的优先级选择最佳管道。利用ToTem，我们能够从超深度靶向基因测序（TGS）数据和全基因组测序（WGS）数据中优化体细胞变异调用。ToTem是一个自动化管道优化工具，可以在https://totem.software上免费获得。本文的在线版本（10.1186/s12859-018-2227-x）包含补充材料，授权用户可以使用。
High-throughput bioinformatics analyses of next generation sequencing (NGS) data often require challenging pipeline optimization. The key problem is choosing appropriate tools and selecting the best parameters for optimal precision and recall. Here we introduce ToTem, a tool for automated pipeline optimization. ToTem is a stand-alone web application with a comprehensive graphical user interface (GUI). ToTem is written in Java and PHP with an underlying connection to a MySQL database. Its primary role is to automatically generate, execute and benchmark different variant calling pipeline settings. Our tool allows an analysis to be started from any level of the process and with the possibility of plugging almost any tool or code. To prevent an over-fitting of pipeline parameters, ToTem ensures the reproducibility of these by using cross validation techniques that penalize the final precision, recall and F-measure. The results are interpreted as interactive graphs and tables allowing an optimal pipeline to be selected, based on the user’s priorities. Using ToTem, we were able to optimize somatic variant calling from ultra-deep targeted gene sequencing (TGS) data and germline variant detection in whole genome sequencing (WGS) data. ToTem is a tool for automated pipeline optimization which is freely available as a web application at https://totem.software. The online version of this article (10.1186/s12859-018-2227-x) contains supplementary material, which is available to authorized users.
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影响因子：
11.4
作者：
Kubesova B;Pavlova S;Malcikova J;Kabathova J;Radova L;Tom N;Tichy B;Plevova K;Kantorova B;Fiedorova K;Slavikova M;Bystry V;Kissova J;Gisslinger B;Gisslinger H;Penka M;Mayer J;Kralovics R;Pospisilova S;Doubek M
通讯作者：
Doubek M
影响因子：
9.5
作者：
Pabinger S;Dander A;Fischer M;Snajder R;Sperk M;Efremova M;Krabichler B;Speicher MR;Zschocke J;Trajanoski Z
通讯作者：
Trajanoski Z
影响因子：
9.8
作者：
Zook JM;Catoe D;McDaniel J;Vang L;Spies N;Sidow A;Weng Z;Liu Y;Mason CE;Alexander N;Henaff E;McIntyre AB;Chandramohan D;Chen F;Jaeger E;Moshrefi A;Pham K;Stedman W;Liang T;Saghbini M;Dzakula Z;Hastie A;Cao H;Deikus G;Schadt E;Sebra R;Bashir A;Truty RM;Chang CC;Gulbahce N;Zhao K;Ghosh S;Hyland F;Fu Y;Chaisson M;Xiao C;Trow J;Sherry ST;Zaranek AW;Ball M;Bobe J;Estep P;Church GM;Marks P;Kyriazopoulou-Panagiotopoulou S;Zheng GX;Schnall-Levin M;Ordonez HS;Mudivarti PA;Giorda K;Sheng Y;Rypdal KB;Salit M
通讯作者：
Salit M
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：
--
影响因子：
4.6
作者：
Hwang S;Kim E;Lee I;Marcotte EM
通讯作者：
Marcotte EM