Motivation: Deep metagenomic sequencing of biological samples has the potential to recover otherwise difficult-to-detect microorganisms and accurately characterize biological samples with limited prior knowledge of sample contents. Existing metagenomic taxonomic classification algorithms, however, do not scale well to analyze large metagenomic datasets, and balancing classification accuracy with computational efficiency presents a fundamental challenge. Results: A method is presented to shift computational costs to an offline computation by creating a taxonomy/genome index that supports scalable metagenomic classification. Scalable performance is demonstrated on real and simulated data to show accurate classification in the presence of novel organisms on samples that include viruses, prokaryotes, fungi and protists. Taxonomic classification of the previously published 150 giga-base Tyrolean Iceman dataset was found to take520 h on a single node 40 core large memory machine and provide new insights on the metagenomic contents of the sample.
Ames, Sasha K., Hysom, David A., Gardner, Shea N., Lloyd, G. Scott, Gokhale, Maya B., & Allen, Jonathan E. (2013). Scalable metagenomic taxonomy classification using a reference genome database. Bioinformatics, 29(18). https://doi.org/10.1093/bioinformatics/btt389
Ames, Sasha K., Hysom, David A., Gardner, Shea N., et al., "Scalable metagenomic taxonomy classification using a reference genome database," Bioinformatics 29, no. 18 (2013), https://doi.org/10.1093/bioinformatics/btt389
@article{osti_1625283,
author = {Ames, Sasha K. and Hysom, David A. and Gardner, Shea N. and Lloyd, G. Scott and Gokhale, Maya B. and Allen, Jonathan E.},
title = {Scalable metagenomic taxonomy classification using a reference genome database},
annote = {Motivation: Deep metagenomic sequencing of biological samples has the potential to recover otherwise difficult-to-detect microorganisms and accurately characterize biological samples with limited prior knowledge of sample contents. Existing metagenomic taxonomic classification algorithms, however, do not scale well to analyze large metagenomic datasets, and balancing classification accuracy with computational efficiency presents a fundamental challenge. Results: A method is presented to shift computational costs to an offline computation by creating a taxonomy/genome index that supports scalable metagenomic classification. Scalable performance is demonstrated on real and simulated data to show accurate classification in the presence of novel organisms on samples that include viruses, prokaryotes, fungi and protists. Taxonomic classification of the previously published 150 giga-base Tyrolean Iceman dataset was found to take520 h on a single node 40 core large memory machine and provide new insights on the metagenomic contents of the sample.},
doi = {10.1093/bioinformatics/btt389},
url = {https://www.osti.gov/biblio/1625283},
journal = {Bioinformatics},
issn = {ISSN 1367-4803},
number = {18},
volume = {29},
place = {United States},
publisher = {International Society for Computational Biology - Oxford University Press},
year = {2013},
month = {07}}