HTSstation: a web application and open-access libraries for high-throughput sequencing data analysis

Fabrice P A David; Julien Delafontaine; Solenne Carat; Frederick J Ross; Gregory Lefebvre; Yohan Jarosz; Lucas Sinclair; Daan Noordermeer; Jacques Rougemont; Marion Leleu

doi:10.1371/journal.pone.0085879

HTSstation: a web application and open-access libraries for high-throughput sequencing data analysis

PLoS One. 2014 Jan 27;9(1):e85879. doi: 10.1371/journal.pone.0085879. eCollection 2014.

Affiliations

¹ School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland ; Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.
² School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland ; Swiss Institute for Experimental Cancer Research (ISREC), Lausanne, Switzerland.
³ School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland ; Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland ; Swiss Institute for Experimental Cancer Research (ISREC), Lausanne, Switzerland.

Abstract

The HTSstation analysis portal is a suite of simple web forms coupled to modular analysis pipelines for various applications of High-Throughput Sequencing including ChIP-seq, RNA-seq, 4C-seq and re-sequencing. HTSstation offers biologists the possibility to rapidly investigate their HTS data using an intuitive web application with heuristically pre-defined parameters. A number of open-source software components have been implemented and can be used to build, configure and run HTS analysis pipelines reactively. Besides, our programming framework empowers developers with the possibility to design their own workflows and integrate additional third-party software. The HTSstation web application is accessible at http://htsstation.epfl.ch.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Computational Biology / methods*
Gene Library*
Genes, Homeobox / genetics
High-Throughput Nucleotide Sequencing / methods*
Internet*
Multigene Family / genetics
Mycobacterium leprae / physiology
Phylogeography
Software*

Grants and funding

This work has been supported by SystemsX.ch, the Swiss Initiative in Systems Biology, through the SyBIT (JD, FJR, LS, YJ), CycliX (JR), LipidX (FPAD) and DynamiX (JR) projects, by the ERC grant SystemsHox.ch to Denis Duboule (DN, ML), by a Swiss National Science Foundation Sinergia Grant CRSI33_130662 to Daniel Constam (SC), and by the EPFL. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.