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bioRxiv · 10.1101/2020.04.30.069732

HPC-REDItools: a Novel HPC-aware Tool for Improved Large Scale RNA-editing Analysis

Flati, T.·Gioiosa, S.·Spallanzani, N.·Tagliaferri, I.·Diroma, M. A.·Pesole, G.·Chillemi, G.·Picardi, E.·Castrignano, T.
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Abstract

BackgroundRNA editing is a widespread co-/post-transcriptional mechanism that alters primary RNA sequences through the modification of specific nucleotides and it can increase both the transcriptome and proteome diversity. The automatic detection of RNA-editing from RNA-seq data is computational intensive and limited to small data sets, thus preventing a reliable genome-wide characterisation of such process. ResultsIn this work we introduce HPC-REDItools, an upgraded tool for accurate RNA-editing events discovery from large dataset repositories. Availability: https://github.com/BioinfoUNIBA/REDItools2. ConclusionsHPC-REDItools is dramatically faster than the previous version, REDItools, enabling big-data analysis by means of a MPI-based implementation and scaling almost linearly with the number of available cores.

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Flati, T., Gioiosa, S., Spallanzani, N., Tagliaferri, I., Diroma, M. A., Pesole, G., Chillemi, G., Picardi, E., Castrignano, T.. 2020-04-30. HPC-REDItools: a Novel HPC-aware Tool for Improved Large Scale RNA-editing Analysis. https://doi.org/10.1101/2020.04.30.069732

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