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

Evaluating Metagenome Assembly on a Simple Defined Community with Many Strain Variants

Sherine Awad, View ORCID ProfileLuiz Irber, View ORCID ProfileC. Titus Brown
doi: https://doi.org/10.1101/155358
Sherine Awad
1Department of Population Health and Reproduction, University of California, Davis Davis, CA 95616 USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Luiz Irber
1Department of Population Health and Reproduction, University of California, Davis Davis, CA 95616 USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Luiz Irber
C. Titus Brown
1Department of Population Health and Reproduction, University of California, Davis Davis, CA 95616 USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for C. Titus Brown
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Preview PDF
Loading

Abstract

We evaluate the performance of three metagenome assemblers, IDBA, MetaSPAdes, and MEGAHIT, on short-read sequencing of a defined “mock” community containing 64 genomes (Shakya et al. (2013)). We update the reference metagenome for this mock community and detect several additional genomes in the read data set. We show that strain confusion results in significant loss in assembly of reference genomes that are otherwise completely present in the read data set. In agreement with previous studies, we find that MEGAHIT performs best computationally; we also show that MEGAHIT tends to recover larger portions of the strain variants than the other assemblers.

Footnotes

  • ↵* E-mail: ctbrown{at}ucdavis.edu

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 July 03, 2017.
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.
Evaluating Metagenome Assembly on a Simple Defined Community with Many Strain Variants
(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
Evaluating Metagenome Assembly on a Simple Defined Community with Many Strain Variants
Sherine Awad, Luiz Irber, C. Titus Brown
bioRxiv 155358; doi: https://doi.org/10.1101/155358
Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
Citation Tools
Evaluating Metagenome Assembly on a Simple Defined Community with Many Strain Variants
Sherine Awad, Luiz Irber, C. Titus Brown
bioRxiv 155358; doi: https://doi.org/10.1101/155358

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 (2441)
  • Biochemistry (4808)
  • Bioengineering (3342)
  • Bioinformatics (14730)
  • Biophysics (6665)
  • Cancer Biology (5194)
  • Cell Biology (7459)
  • Clinical Trials (138)
  • Developmental Biology (4388)
  • Ecology (6906)
  • Epidemiology (2057)
  • Evolutionary Biology (9948)
  • Genetics (7360)
  • Genomics (9555)
  • Immunology (4589)
  • Microbiology (12741)
  • Molecular Biology (4969)
  • Neuroscience (28451)
  • Paleontology (199)
  • Pathology (811)
  • Pharmacology and Toxicology (1400)
  • Physiology (2034)
  • Plant Biology (4528)
  • Scientific Communication and Education (981)
  • Synthetic Biology (1307)
  • Systems Biology (3923)
  • Zoology (731)