QUARTIC: QUick pArallel algoRithms for high-Throughput sequencIng data proCessing [version 3; peer review: 2 approved]

Life science has entered the so-called 'big data era' where biologists, clinicians and bioinformaticians are overwhelmed with high-throughput sequencing data. While they offer new insights to decipher the genome structure they also raise major challenges to use them for daily clinical prac...

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Published inF1000 research Vol. 9; p. 240
Main Authors Jarlier, Frédéric, Joly, Nicolas, Fedy, Nicolas, Magalhaes, Thomas, Sirotti, Leonor, Paganiban, Paul, Martin, Firmin, McManus, Michael, Hupé, Philippe
Format Journal Article
LanguageEnglish
Published England Faculty of 1000 Ltd 2020
F1000 Research Limited
F1000 Research Ltd
Subjects
Algorithms
Computer programs
Computing Methodologies
Data analysis
Genomes
Genomics
High-Throughput Nucleotide Sequencing
Next-generation sequencing
Reproducibility of Results
Software
Software Tool
Supercomputers
High-Throughput Sequencing
High-Performance Computing
Alignment
MPI
Sorting
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Summary:Life science has entered the so-called 'big data era' where biologists, clinicians and bioinformaticians are overwhelmed with high-throughput sequencing data. While they offer new insights to decipher the genome structure they also raise major challenges to use them for daily clinical practice care and diagnosis purposes as they are bigger and bigger. Therefore, we implemented a software to reduce the time to delivery for the alignment and the sorting of high-throughput sequencing data.  Our solution is implemented using Message Passing Interface and is intended for high-performance computing architecture. The software scales linearly with respect to the size of the data and ensures a total reproducibility with the traditional tools. For example, a 300X whole genome can be aligned and sorted within less than 9 hours with 128 cores. The software offers significant speed-up using multi-cores and multi-nodes parallelization.
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F.J. and N.J. developed and tested mpiBWA. F.J., N.F., L.S., T.M, P.P. and F.M. developed and tested mpiSORT. M.M. provided technical expertise and access to computing cluster facilities to benchmark the code. F.J. coordinated the developments. F.J. and P.H. wrote the manuscript. P.H. supervised the study.
Competing interests: The authors declare that Institut Curie and Intel Corporation have a partnership.
ISSN:2046-1402
2046-1402
DOI:10.12688/f1000research.22954.3