Colib'read on galaxy : a tools suite dedicated to biological information extraction from raw NGS reads

Background: With next-generation sequencing (NGS) technologies, the life sciences face a deluge of raw data. Classical analysis processes for such data often begin with an assembly step, needing large amounts of computing resources, and potentially removing or modifying parts of the biological information contained in the data. Our approach proposes to focus directly on biological questions, by considering raw unassembled NGS data, through a suite of six command-line tools. Findings: Dedicated to 'whole-genome assembly-free' treatments, the Colib'read tools suite uses optimized algorithms for various analyses of NGS datasets, such as variant calling or read set comparisons. Based on the use of a de Bruijn graph and bloom filter, such analyses can be performed in a few hours, using small amounts of memory. Applications using real data demonstrate the good accuracy of these tools compared to classical approaches. To facilitate data analysis and tools dissemination, we developed Galaxy tools and tool shed repositories. Conclusions: With the Colib'read Galaxy tools suite, we enable a broad range of life scientists to analyze raw NGS data. More importantly, our approach allows the maximum biological information to be retained in the data, and uses a very low memory footprint.Peer reviewe

Monte Carlo simulation on Graphical Processor Unit of the scattered beam in radiography non-destructive testing context

CEA-LIST develops CIVA software for non-destructive testing simulation. Radiography Monte Carlo simulation for the scattered beam can be quite long (several hours) even on a multi-thread CPU implementation. In order to reduce this computation time, we have modified and adapted for CIVA a GPU open source code named MCGPU. This paper presents our work and the results of cross comparison between CIVA and the modified MCGPU code in a NDT context