Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Sanger Sequencing01:57

Sanger Sequencing

760.1K
DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
760.1K
Next-generation Sequencing03:00

Next-generation Sequencing

93.4K
The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
93.4K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

A call for the United States to continue investing in science.

ASM case reports·2025
Same author

A call for healing and unity.

ASM case reports·2025
Same author

A call for healing and unity.

Microbiology resource announcements·2025
Same author

A call for the United States to continue investing in science.

Journal of bacteriology·2025
Same author

A call for healing and unity.

Microbiology and molecular biology reviews : MMBR·2025
Same author

A call for healing and unity.

Journal of bacteriology·2025

Related Experiment Video

Updated: Oct 4, 2025

Next-generation Sequencing of 16S Ribosomal RNA Gene Amplicons
10:24

Next-generation Sequencing of 16S Ribosomal RNA Gene Amplicons

Published on: August 29, 2014

83.8K

OptiFit: an Improved Method for Fitting Amplicon Sequences to Existing OTUs.

Kelly L Sovacool1, Sarah L Westcott2, M Brodie Mumphrey1

  • 1Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.

Msphere
|February 2, 2022
PubMed
Summary

We developed OptiFit, a new algorithm for assigning microbial sequences to operational taxonomic units (OTUs). OptiFit provides consistent and high-quality OTU assignments, improving microbial community analysis across studies.

Keywords:
16S rRNA genebioinformaticsclusteringmetagenomicsmicrobial ecologymicrobiome

More Related Videos

Validating Whole Genome Nanopore Sequencing, using Usutu Virus as an Example
05:45

Validating Whole Genome Nanopore Sequencing, using Usutu Virus as an Example

Published on: March 11, 2020

9.0K
Rare Event Detection Using Error-corrected DNA and RNA Sequencing
10:36

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Published on: August 3, 2018

12.2K

Related Experiment Videos

Last Updated: Oct 4, 2025

Next-generation Sequencing of 16S Ribosomal RNA Gene Amplicons
10:24

Next-generation Sequencing of 16S Ribosomal RNA Gene Amplicons

Published on: August 29, 2014

83.8K
Validating Whole Genome Nanopore Sequencing, using Usutu Virus as an Example
05:45

Validating Whole Genome Nanopore Sequencing, using Usutu Virus as an Example

Published on: March 11, 2020

9.0K
Rare Event Detection Using Error-corrected DNA and RNA Sequencing
10:36

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Published on: August 3, 2018

12.2K

Area of Science:

  • Microbiology
  • Bioinformatics
  • Computational Biology

Background:

  • Assigning amplicon sequences to operational taxonomic units (OTUs) is crucial for microbial community analysis.
  • Existing methods like de novo clustering can yield inconsistent OTU assignments when new data is added.
  • Reference-based methods offer consistency but often produce lower-quality assignments compared to de novo approaches.

Purpose of the Study:

  • To develop an efficient algorithm, OptiFit, for assigning sequences to existing OTUs without re-clustering entire datasets.
  • To provide a method that balances the consistency of reference-based clustering with the quality of de novo methods.
  • To enable seamless integration of new samples into existing microbial community datasets for comparative analyses.

Main Methods:

  • Developed the OptiFit algorithm, inspired by the de novo OptiClust algorithm.
  • OptiFit considers pairwise similarities between reference and query sequences for improved OTU assignment.
  • Evaluated OptiFit using four datasets with strategies including direct database clustering and a reference-query split approach.

Main Results:

  • OptiFit produces OTUs of quality comparable to de novo methods like OptiClust.
  • When using a reference-query split strategy, OptiFit achieves faster processing speeds.
  • The algorithm demonstrates improved performance in reference-based clustering, maintaining high assignment quality.

Conclusions:

  • OptiFit offers an efficient and high-quality solution for consistent OTU assignment in microbial ecology.
  • It addresses the limitations of existing methods, enabling robust cross-study comparisons and data integration.
  • OptiFit is suitable for researchers needing reliable and consistent microbial community characterization.