HPC-REDItools: a novel HPC-aware tool for improved large scale RNA-editing analysis

Autor:	Tiziano Flati, Silvia Gioiosa, Nicola Spallanzani, Ilario Tagliaferri, Maria Angela Diroma, Graziano Pesole, Giovanni Chillemi, Ernesto Picardi, Tiziana Castrignanò
Jazyk:	angličtina
Rok vydání:	2020
Předmět:	RNA-editing High Performance Computing REDItools Next Generation Sequencing Sequence Analysis Bioinformatics pipeline Computer applications to medicine. Medical informatics R858-859.7 Biology (General) QH301-705.5
Zdroj:	BMC Bioinformatics, Vol 21, Iss S10, Pp 1-12 (2020)
Druh dokumentu:	article
ISSN:	1471-2105
DOI:	10.1186/s12859-020-03562-x
Popis:	Abstract Background RNA 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. Results In 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 . Conclusions HPC-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.
Databáze:	Directory of Open Access Journals
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