BioLite, a Lightweight Bioinformatics Framework with Automated Tracking of Diagnostics and Provenance

Authors: 

Mark Howison, Nicholas A. Sinnott-Armstrong, and Casey W. Dunn, Brown University

Abstract: 

We present a new Python/C++ framework, BioLite, for implementing bioinformatics pipelines for Next-Generation Sequencing (NGS) data. BioLite tracks provenance of analyses, automates the collection and reporting of diagnostics (such as summary statistics and plots at intermediate stages), and profiles computational requirements. These diagnostics can be accessed across multiple stages of a pipeline, from other pipelines, and in HTML reports. Finally, we describe several use cases for diagnostics in our own analyses.

 

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BibTeX
@inproceedings {179544,
title = {BioLite, a Lightweight Bioinformatics Framework with Automated Tracking of Diagnostics and Provenance},
booktitle = {4th {USENIX} Workshop on the Theory and Practice of Provenance (TaPP 12)},
year = {2012},
address = {Boston, MA},
url = {https://www.usenix.org/conference/tapp12/workshop-program/presentation/Howison},
publisher = {{USENIX} Association},
month = jun,
}

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