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

phyloFlash – Rapid SSU rRNA profiling and targeted assembly from metagenomes

View ORCID ProfileHarald R. Gruber-Vodicka, View ORCID ProfileBrandon K. B. Seah, View ORCID ProfileElmar Pruesse
doi: https://doi.org/10.1101/521922
Harald R. Gruber-Vodicka
1Max Planck Institute for Marine Microbiology, Celsiusstraße 1, Bremen 28359, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Harald R. Gruber-Vodicka
  • For correspondence: hgruber@mpi-bremen.de
Brandon K. B. Seah
1Max Planck Institute for Marine Microbiology, Celsiusstraße 1, Bremen 28359, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Brandon K. B. Seah
Elmar Pruesse
2Department of Medicine, Division of Biomedical Informatics and Personalized Medicine, University of Colorado Denver Anschutz Medical Campus, Aurora, CO 80045, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Elmar Pruesse
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Preview PDF
Loading

ABSTRACT

The SSU rRNA gene is the key marker in molecular ecology for all domains of life, but is largely absent from metagenome-assembled genomes that often are the only resource available for environmental microbes. Here we present phyloFlash, a pipeline to overcome this gap with rapid, SSU rRNA-centered taxonomic classification, targeted assembly, and graph-based binning of full metagenomic assemblies. We show that a cleanup of artifacts is pivotal even with a curated reference database. With such a filtered database, the general-purpose mapper BBmap extracts SSU rRNA reads five times faster than the rRNA-specialized tool SortMeRNA with similar sensitivity and higher selectivity on simulated metagenomes. Reference-based targeted assemblers yielded either highly fragmented assemblies or high levels of chimerism, so we employ the general-purpose genomic assembler SPAdes. Our optimized implementation is independent of reference database composition and has satisfactory levels of chimera formation. Using the phyloFlash workflow we could recover the first complete genomes of several enigmatic taxa, including Marinamargulisbacteria from surface ocean seawater. phyloFlash quickly processes Illumina (meta)genomic data, is straightforward to use, even as part of high-throughput quality control, and has user-friendly output reports. The software is available at https://github.com/HRGV/phyloFlash (GPL3 license) and is documented with an online manual.

Footnotes

  • ↵3 The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.

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-NC-ND 4.0 International license.
Back to top
PreviousNext
Posted January 17, 2019.
Download PDF

Supplementary Material

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.
phyloFlash – Rapid SSU rRNA profiling and targeted assembly from metagenomes
(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
phyloFlash – Rapid SSU rRNA profiling and targeted assembly from metagenomes
Harald R. Gruber-Vodicka, Brandon K. B. Seah, Elmar Pruesse
bioRxiv 521922; doi: https://doi.org/10.1101/521922
Reddit logo Twitter logo Facebook logo LinkedIn logo Mendeley logo
Citation Tools
phyloFlash – Rapid SSU rRNA profiling and targeted assembly from metagenomes
Harald R. Gruber-Vodicka, Brandon K. B. Seah, Elmar Pruesse
bioRxiv 521922; doi: https://doi.org/10.1101/521922

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 (4838)
  • Biochemistry (10734)
  • Bioengineering (8013)
  • Bioinformatics (27174)
  • Biophysics (13935)
  • Cancer Biology (11080)
  • Cell Biology (15984)
  • Clinical Trials (138)
  • Developmental Biology (8757)
  • Ecology (13232)
  • Epidemiology (2067)
  • Evolutionary Biology (17309)
  • Genetics (11665)
  • Genomics (15882)
  • Immunology (10989)
  • Microbiology (25989)
  • Molecular Biology (10608)
  • Neuroscience (56326)
  • Paleontology (417)
  • Pathology (1727)
  • Pharmacology and Toxicology (2998)
  • Physiology (4529)
  • Plant Biology (9588)
  • Scientific Communication and Education (1610)
  • Synthetic Biology (2671)
  • Systems Biology (6959)
  • Zoology (1507)