KNIME4NGS: a comprehensive toolbox for next generation sequencing analysis

被引：4

作者：

Hastreiter, Maximilian ^{[1
]}

Jeske, Tim ^{[1
]}

Hoser, Jonathan ^{[1
]}

Kluge, Michael ^{[1
]}

Ahomaa, Kaarin ^{[1
]}

Friedl, Marie-Sophie ^{[1
]}

Kopetzky, Sebastian J. ^{[1
]}

Quell, Jan-Dominik ^{[1
]}

Mewes, H. -Werner ^{[1
]}

Kueffner, Robert ^{[1
]}

机构：

[1] Helmholtz Zentrum Munchen, Inst Bioinformat & Syst Biol, D-85764 Neuherberg, Germany

来源：

BIOINFORMATICS | 2017年 / 33卷 / 10期

关键词：

D O I：

10.1093/bioinformatics/btx003

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

A Summary: Analysis of Next Generation Sequencing (NGS) data requires the processing of large datasets by chaining various tools with complex input and output formats. In order to automate data analysis, we propose to standardize NGS tasks into modular workflows. This simplifies reliable handling and processing of NGS data, and corresponding solutions become substantially more reproducible and easier to maintain. Here, we present a documented, linux-based, toolbox of 42 processing modules that are combined to construct workflows facilitating a variety of tasks such as DNAseq and RNAseq analysis. We also describe important technical extensions. The high throughput executor (HTE) helps to increase the reliability and to reduce manual interventions when processing complex datasets. We also provide a dedicated binary manager that assists users in obtaining the modules' executables and keeping them up to date. As basis for this actively developed toolbox we use the workflow management software KNIME.

引用

页码：1565 / 1567

页数：3

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