Alignment-free Genomic Analysis via a Big Data Spark Platform

Raffaele Giancarlo, Umberto Ferraro Petrillo, Francesco Palini, Umberto Ferraro Petrillo, Giuseppe Cattaneo, Umberto Ferraro Petrillo

Research output: Contribution to journalArticlepeer-review

Abstract

Motivation: Alignment-free distance and similarity functions (AF functions, for short) are a well-established alternative to pairwise and multiple sequence alignments for many genomic, metagenomic and epigenomic tasks. Due to data-intensive applications, the computation of AF functions is a Big Data problem, with the recent literature indicating that the development of fast and scalable algorithms computing AF functions is a high-priority task. Somewhat surprisingly, despite the increasing popularity of Big Data technologies in computational biology, the development of a Big Data platform for those tasks has not been pursued, possibly due to its complexity.Results: We fill this important gap by introducing FADE, the first extensible, efficient and scalable Spark platform for alignment-free genomic analysis. It supports natively eighteen of the best performing AF functions coming out of a recent hallmark benchmarking study. FADE development and potential impact comprises novel aspects of interest. Namely, (i) a considerable effort of distributed algorithms, the most tangible result being a much faster execution time of reference methods like MASH and FSWM; (ii) a software design that makes FADE user-friendly and easily extendable by Spark non-specialists; (iii) its ability to support data- and compute-intensive tasks. About this, we provide a novel and much needed analysis of how informative and robust AF functions are, in terms of the statistical significance of their output. Our findings naturally extend the ones of the highly regarded benchmarking study, since the functions that can really be used are reduced to a handful of the eighteen included in FADE.
Original languageEnglish
Pages (from-to)1658-1665
Number of pages8
JournalBioinformatics
Volume37
Publication statusPublished - 2021

All Science Journal Classification (ASJC) codes

  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics
  • Statistics and Probability
  • Biochemistry
  • Molecular Biology

Fingerprint

Dive into the research topics of 'Alignment-free Genomic Analysis via a Big Data Spark Platform'. Together they form a unique fingerprint.

Cite this