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.
Highlights
High-throughput sequencing (HTS) has produced a major shift in the amount and speed of data production in genomics
To illustrate the analysis capabilities of HTSstation, we detail below a number of specific cases that we have selected from relevant publications having used early versions of these pipelines
The transcriptional repressor Kap1 was shown to mediate silencing of endogenous retro-viruses (ERV) in mouse embryonic stem (ES) cells [7], as deduced from comparing the transcriptomes of wild-type and Kap1 knockout ES cells
Summary
Background High-throughput sequencing (HTS) has produced a major shift in the amount and speed of data production in genomics. The importance of bioinformatics has grown in parallel and with it the necessity to implement efficient and reproducible analysis processes adapted to each particular application. The academic world generates a wealth of freely available software and this must be exploited for the sake of efficiency without preconceptions of programming language, platform or style. In this context, we have undertaken to implement an analysis platform that helps us flexibly introduce our own innovations sideby-side with publicly available tools and make them accessible to the scientific community.
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