FastSpar: rapid and scalable correlation estimation for compositional data

Bioinformatics
Stephen C WattsKathryn E Holt

Abstract

A common goal of microbiome studies is the elucidation of community composition and member interactions using counts of taxonomic units extracted from sequence data. Inference of interaction networks from sparse and compositional data requires specialized statistical approaches. A popular solution is SparCC, however its performance limits the calculation of interaction networks for very high-dimensional datasets. Here we introduce FastSpar, an efficient and parallelizable implementation of the SparCC algorithm which rapidly infers correlation networks and calculates P-values using an unbiased estimator. We further demonstrate that FastSpar reduces network inference wall time by 2-3 orders of magnitude compared to SparCC. FastSpar source code, precompiled binaries and platform packages are freely available on GitHub: github.com/scwatts/FastSpar. Supplementary data are available at Bioinformatics online.

References

Nov 4, 2010·Statistical Applications in Genetics and Molecular Biology·Belinda Phipson, Gordon K Smyth
Oct 3, 2012·PLoS Computational Biology·Jonathan Friedman, Eric J Alm
Aug 27, 2013·Applied and Environmental Microbiology·Sarah P PreheimEric J Alm
Mar 27, 2015·Applied Microbiology and Biotechnology·Feng Ju, Tong Zhang
Oct 31, 2015·Nature Communications·Geicho NakatsuJoseph J Y Sung
May 31, 2017·Academic Medicine : Journal of the Association of American Medical Colleges·Desmond B Teo

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Citations

Apr 28, 2020·Nucleic Acids Research·Sunil NagpalSharmila S Mande
Mar 4, 2020·Journal of Animal Science and Biotechnology·Bruno G N AndradeLuciana C A Regitano
Sep 9, 2020·Scientific Reports·Tomás Gomes Reis VelosoLucas Louzada Pereira
Apr 22, 2020·Microbiome·Ramiro LogaresRamon Massana
Nov 28, 2020·Molecular Ecology Resources·Didac Barroso-BergadàCorinne Vacher
Jan 23, 2021·Proceedings of the National Academy of Sciences of the United States of America·Kirsten E PoffEdward F DeLong
Feb 26, 2021·Nature·Chitong RaoSeth Rakoff-Nahoum
Apr 6, 2021·Frontiers in Microbiology·Maria Paz VenteroJuan Carlos Rodríguez
Apr 9, 2021·Frontiers in Microbiology·Ahmad Nuruddin KhoiriSawannee Sutheeworapong
Aug 17, 2021·Environmental Microbiology·Cristina BezVittorio Venturi
Sep 9, 2021·MSphere·Teresa TavellaSimone Rampelli
Sep 7, 2021·Frontiers in Microbiology·Daniel LoosGianni Panagiotou
Nov 19, 2021·The Science of the Total Environment·Jing LiBrajesh K Singh

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Software Mentioned

GNU
LAPACK
mothur
GSL
OpenMP
FastSpar
numpy
Python
Ubuntu
SparCC

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