Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

Exploring neighborhoods in large metagenome assembly graphs reveals hidden sequence diversity

View ORCID ProfileC. Titus Brown, View ORCID ProfileDominik Moritz, View ORCID ProfileMichael P. O’Brien, View ORCID ProfileFelix Reidl, View ORCID ProfileTaylor Reiter, View ORCID ProfileBlair D. Sullivan
doi: https://doi.org/10.1101/462788
C. Titus Brown
aDepartment of Population Health and Reproduction, University of California Davis
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for C. Titus Brown
  • For correspondence: ctbrown@ucdavis.edu vbsulliv@ncsu.edu
Dominik Moritz
bPaul G. Allen School of Computer Science and Engineering, University of Washington
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Dominik Moritz
Michael P. O’Brien
cDepartment of Computer Science, NC State University
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Michael P. O’Brien
Felix Reidl
cDepartment of Computer Science, NC State University
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Felix Reidl
Taylor Reiter
aDepartment of Population Health and Reproduction, University of California Davis
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Taylor Reiter
Blair D. Sullivan
cDepartment of Computer Science, NC State University
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Blair D. Sullivan
  • For correspondence: ctbrown@ucdavis.edu vbsulliv@ncsu.edu
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Preview PDF
Loading

Abstract

Genomes computationally inferred from large metagenomic data sets are often incomplete and may be missing functionally important content and strain variation. We introduce an information retrieval system for large metagenomic data sets that exploits the sparsity of DNA assembly graphs to efficiently extract subgraphs surrounding an inferred genome. We apply this system to recover missing content from genome bins and show that substantial genomic sequence variation is present in a real metagenome. Our software implementation is available at https://github.com/spacegraphcats/ spacegraphcats under the 3-Clause BSD License.

Footnotes

  • DM, MPO, FR, and BDS designed and implemented algorithms; CTB, DM, MPO, and FR developed software; CTB and TR conducted biological data analysis; CTB and BDS supervised work. All authors interpreted results, wrote text, created figures, and approved the submitted paper.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
Back to top
PreviousNext
Posted March 13, 2019.
Download PDF
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Exploring neighborhoods in large metagenome assembly graphs reveals hidden sequence diversity
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Exploring neighborhoods in large metagenome assembly graphs reveals hidden sequence diversity
C. Titus Brown, Dominik Moritz, Michael P. O’Brien, Felix Reidl, Taylor Reiter, Blair D. Sullivan
bioRxiv 462788; doi: https://doi.org/10.1101/462788
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
Exploring neighborhoods in large metagenome assembly graphs reveals hidden sequence diversity
C. Titus Brown, Dominik Moritz, Michael P. O’Brien, Felix Reidl, Taylor Reiter, Blair D. Sullivan
bioRxiv 462788; doi: https://doi.org/10.1101/462788

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Bioinformatics
Subject Areas
All Articles
  • Animal Behavior and Cognition (3580)
  • Biochemistry (7534)
  • Bioengineering (5488)
  • Bioinformatics (20709)
  • Biophysics (10267)
  • Cancer Biology (7942)
  • Cell Biology (11597)
  • Clinical Trials (138)
  • Developmental Biology (6576)
  • Ecology (10151)
  • Epidemiology (2065)
  • Evolutionary Biology (13565)
  • Genetics (9504)
  • Genomics (12801)
  • Immunology (7891)
  • Microbiology (19472)
  • Molecular Biology (7624)
  • Neuroscience (41939)
  • Paleontology (307)
  • Pathology (1253)
  • Pharmacology and Toxicology (2182)
  • Physiology (3254)
  • Plant Biology (7017)
  • Scientific Communication and Education (1291)
  • Synthetic Biology (1944)
  • Systems Biology (5412)
  • Zoology (1109)