TY - JOUR
T1 - KNIME4NGS
T2 - A comprehensive toolbox for next generation sequencing analysis
AU - Hastreiter, Maximilian
AU - Jeske, Tim
AU - Hoser, Jonathan
AU - Kluge, Michael
AU - Ahomaa, Kaarin
AU - Friedl, Marie Sophie
AU - Kopetzky, Sebastian J.
AU - Quell, Jan Dominik
AU - Mewes, H. Werner
AU - Küffner, Robert
N1 - Publisher Copyright:
© The Author 2017.
PY - 2017/5/15
Y1 - 2017/5/15
N2 - 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. Availability and Implementation: See http://ibisngs.github.io/knime4ngs for nodes and user manual (GPLv3 license) .
AB - 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. Availability and Implementation: See http://ibisngs.github.io/knime4ngs for nodes and user manual (GPLv3 license) .
UR - http://www.scopus.com/inward/record.url?scp=85020285279&partnerID=8YFLogxK
U2 - 10.1093/bioinformatics/btx003
DO - 10.1093/bioinformatics/btx003
M3 - Article
C2 - 28069593
AN - SCOPUS:85020285279
SN - 1367-4803
VL - 33
SP - 1565
EP - 1567
JO - Bioinformatics
JF - Bioinformatics
IS - 10
ER -