riboviz: analysis and visualization of ribosome profiling datasets.

Carja O, Xing T, Plotkin JB, and Shah P.

bioRxiv : 10.1101/100032

2017

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Abstract

Using high-throughput sequencing to monitor translation in vivo, ribosome profiling can provide critical insights into the dynamics and regulation of protein synthesis in a cell. Since its introduction in 2009, this technique has played a key role in driving biological discovery, and yet it requires a rigorous computational toolkit for widespread adoption. We developed a processing pipeline and browser-based visualization, riboviz, that allows convenient exploration and analysis of riboseq datasets. In implementation, riboviz consists of a comprehensive and flexible backend analysis pipeline that allows the user to analyze their private unpublished dataset, along with a web application for comparison with previously published public datasets. Availability and implementation: JavaScript and R source code and extra documentation are freely available from GitHub, while the web-application is live at riboviz.