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

PUMA: A tool for processing 16S rRNA taxonomy data for analysis and visualization

View ORCID ProfileKeith Mitchell, Christopher Dao, Amanda Freise, View ORCID ProfileSerghei Mangul, View ORCID ProfileJordan Moberg Parker
doi: https://doi.org/10.1101/482380
Keith Mitchell
1Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Keith Mitchell
Christopher Dao
1Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Amanda Freise
1Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Serghei Mangul
2Department of Computer Science, University of California Los Angeles, Los Angeles, CA 90095, USA
3Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, CA, 90095, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Serghei Mangul
Jordan Moberg Parker
1Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Jordan Moberg Parker
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Preview PDF
Loading

Abstract

Microbial community profiling and functional inference via 16S rRNA analysis is quickly expanding across various areas of microbiology due to improvements to technology. There are numerous platforms for producing 16S rRNA taxonomic data which often vary in file and sequence formatting, creating a common barrier in microbiome studies. Additionally, many of the methods for analyzing and visualizing this sequencing data each require their own specific formatting. As a result, efficient and reproducible comparative analysis of taxonomic data and corresponding metadata in multiple programs remains a challenge in the investigation of microbial communities. PUMA, the Program for Unifying Microbiome Analysis, alleviates this problem in microbiome studies by allowing users to take advantage of numerous 16S rRNA taxonomic identification platforms and analysis tools in an efficient manner. PUMA accepts sequencing results from several taxonomic identification platforms and then automates configuration of data and file types for analysis and visualization via many popular tools. The protocol accomplishes this by producing a variety of properly configured, annotated, and altered files for both analysis and visualization of taxonomic community profiles and inferred functional profiles. PUMA provides an easy and flexible interface to accommodate for a variety of users to produce all files needed for all-inclusive analysis of targeted amplicon sequencing studies. PUMA is an unprecedented open-source solution for unifying multiple microbiome analysis softwares and uses an adaptable implementation with the potential to improve and consolidate the state of microbiome research.

Body/Findings

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 November 29, 2018.
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.
PUMA: A tool for processing 16S rRNA taxonomy data for analysis and visualization
(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
PUMA: A tool for processing 16S rRNA taxonomy data for analysis and visualization
Keith Mitchell, Christopher Dao, Amanda Freise, Serghei Mangul, Jordan Moberg Parker
bioRxiv 482380; doi: https://doi.org/10.1101/482380
Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
Citation Tools
PUMA: A tool for processing 16S rRNA taxonomy data for analysis and visualization
Keith Mitchell, Christopher Dao, Amanda Freise, Serghei Mangul, Jordan Moberg Parker
bioRxiv 482380; doi: https://doi.org/10.1101/482380

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

  • Microbiology
Subject Areas
All Articles
  • Animal Behavior and Cognition (2533)
  • Biochemistry (4975)
  • Bioengineering (3486)
  • Bioinformatics (15229)
  • Biophysics (6908)
  • Cancer Biology (5395)
  • Cell Biology (7751)
  • Clinical Trials (138)
  • Developmental Biology (4539)
  • Ecology (7157)
  • Epidemiology (2059)
  • Evolutionary Biology (10233)
  • Genetics (7516)
  • Genomics (9790)
  • Immunology (4860)
  • Microbiology (13231)
  • Molecular Biology (5142)
  • Neuroscience (29464)
  • Paleontology (203)
  • Pathology (838)
  • Pharmacology and Toxicology (1465)
  • Physiology (2142)
  • Plant Biology (4754)
  • Scientific Communication and Education (1013)
  • Synthetic Biology (1338)
  • Systems Biology (4014)
  • Zoology (768)