To Petabytes and beyond: Recent advances in probabilistic and signal processing algorithms and their application to metagenomics

R. A.Leo Elworth, Qi Wang, Pavan K. Kota, C. J. Barberan, Benjamin Coleman, Advait Balaji, Gaurav Gupta, Richard G. Baraniuk, Anshumali Shrivastava, Todd J. Treangen

Research output: Contribution to journalReview article

Abstract

As computational biologists continue to be inundated by ever increasing amounts of metagenomic data, the need for data analysis approaches that keep up with the pace of sequence archives has remained a challenge. In recent years, the accelerated pace of genomic data availability has been accompanied by the application of a wide array of highly efficient approaches from other fields to the field of metagenomics. For instance, sketching algorithms such as MinHash have seen a rapid and widespread adoption. These techniques handle increasingly large datasets with minimal sacrifices in quality for tasks such as sequence similarity calculations. Here, we briefly review the fundamentals of the most impactful probabilistic and signal processing algorithms. We also highlight more recent advances to augment previous reviews in these areas that have taken a broader approach. We then explore the application of these techniques to metagenomics, discuss their pros and cons, and speculate on their future directions.

Original languageEnglish (US)
Pages (from-to)5217-5234
Number of pages18
JournalNucleic Acids Research
Volume48
Issue number10
DOIs
StatePublished - 2020

ASJC Scopus subject areas

  • Genetics

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