MIT Libraries homeMIT Libraries logoDSpace@MIT

MIT
View Item 
  • DSpace@MIT Home
  • MIT Open Access Articles
  • MIT Open Access Articles
  • View Item
  • DSpace@MIT Home
  • MIT Open Access Articles
  • MIT Open Access Articles
  • View Item
JavaScript is disabled for your browser. Some features of this site may not work without it.

Metagenomic binning through low-density hashing

Author(s)
Luo, Yunan; Yu, Yun William; Zeng, Jianyang; Berger Leighton, Bonnie; Peng, Jian
Thumbnail
DownloadPublished version (365.2Kb)
Terms of use
Creative Commons Attribution NonCommercial License 4.0 https://creativecommons.org/licenses/by-nc/4.0/
Metadata
Show full item record
Abstract
Motivation: Vastly greater quantities of microbial genome data are being generated where environmental samples mix together the DNA from many different species. Here, we present Opal for metagenomic binning, the task of identifying the origin species of DNA sequencing reads. We introduce low-density' locality sensitive hashing to bioinformatics, with the addition of Gallager codes for even coverage, enabling quick and accurate metagenomic binning. Results: On public benchmarks, Opal halves the error on precision/recall (F1-score) as compared with both alignment-based and alignment-free methods for species classification. We demonstrate even more marked improvement at higher taxonomic levels, allowing for the discovery of novel lineages. Furthermore, the innovation of low-density, even-coverage hashing should itself prove an essential methodological advance as it enables the application of machine learning to other bioinformatic challenges. Availability and implementation: Full source code and datasets are available at http://opal.csail.mit.edu and https://github.com/yunwilliamyu/opal. Supplementary information: Supplementary data are available at Bioinformatics online.
Date issued
2018-07-13
URI
https://hdl.handle.net/1721.1/122806
Department
Massachusetts Institute of Technology. Department of Mathematics; Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory
Journal
Bioinformatics
Publisher
Oxford University Press (OUP)
Citation
Lou, Yunan, et al. "Metagenomic binning through low-density hashing." Bioinformatics 35, 2, (January 2019): 219–226 © 2018 The Author(s)
Version: Final published version
ISSN
1367-4803
1460-2059

Collections
  • MIT Open Access Articles

Browse

All of DSpaceCommunities & CollectionsBy Issue DateAuthorsTitlesSubjectsThis CollectionBy Issue DateAuthorsTitlesSubjects

My Account

Login

Statistics

OA StatisticsStatistics by CountryStatistics by Department
MIT Libraries homeMIT Libraries logo

Find us on

Twitter Facebook Instagram YouTube RSS

MIT Libraries navigation

SearchHours & locationsBorrow & requestResearch supportAbout us
PrivacyPermissionsAccessibility
MIT
Massachusetts Institute of Technology
Content created by the MIT Libraries, CC BY-NC unless otherwise noted. Notify us about copyright concerns.