PuSH - Publikationsserver des Helmholtz Zentrums München

Hastreiter, M. ; Jeske, T. ; Hoser, J.D.S. ; Kluge, M. ; Ahomaa, K. ; Friedl, M.-S. ; Kopetzky, S.J. ; Quell, J. ; Mewes, H.-W. ; Küffner, R.

KNIME4NGS: A comprehensive toolbox for next generation sequencing analysis.

Bioinformatics 33, 1565-1567 (2017)
Verlagsversion Forschungsdaten DOI PMC
Open Access Green möglich sobald Postprint bei der ZB eingereicht worden ist.
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.
Altmetric
Weitere Metriken?
[➜Einloggen]
Zusatzinfos bearbeiten [➜Einloggen]
Publikationstyp Artikel: Journalartikel
Dokumenttyp Wissenschaftlicher Artikel
Korrespondenzautor
ISSN (print) / ISBN 1367-4803
e-ISSN 1367-4811
Zeitschrift Bioinformatics
Quellenangaben Band: 33, Heft: 10, Seiten: 1565-1567 Artikelnummer: , Supplement: ,
Verlag Oxford University Press
Verlagsort Oxford
Nichtpatentliteratur Publikationen
Begutachtungsstatus Peer reviewed
Institut(e) Institute of Bioinformatics and Systems Biology (IBIS)