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

Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

5.8K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
5.8K
Microbial Classification System01:24

Microbial Classification System

45
Classification is the process of organizing organisms into hierarchically inclusive groups based on their phenotypic similarities or evolutionary relationships. A species comprises one or more strains, and closely related species are grouped into genera. Genera are further classified into families, families into orders, orders into classes, and so forth, up to the domain level, which is the broadest taxonomic rank derived from a combination of phenotypic and genotypic data.The nomenclature of...
45
Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

52
Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
52
Applications of Molecular Taxonomy01:20

Applications of Molecular Taxonomy

41
Molecular taxonomy has revolutionized the understanding and classification of bacteria, providing precise insights into their diversity, evolutionary relationships, and ecological roles. By utilizing molecular techniques such as DNA sequencing and fingerprinting, researchers have made significant strides in various fields related to bacterial studies.Resolving Taxonomic AmbiguitiesMolecular taxonomy has been instrumental in distinguishing closely related bacterial species initially thought to...
41
Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes02:16

Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes

12.5K
The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...
12.5K
Genomics02:02

Genomics

36.5K
Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
36.5K

You might also read

Related Articles

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

Sort by
Same author

Efficient evidence-based genome annotation with EviAnn.

Nature methods·2026
Same author

Testing the reliability of AI-generated protein structures.

bioRxiv : the preprint server for biology·2026
Same author

A complete human pancreatic cancer genome.

bioRxiv : the preprint server for biology·2026
Same author

Comparison of unbiased metagenomic next generation sequencing to targeted multiplex diagnostic assays for the detection of respiratory viruses.

PloS one·2026
Same author

Evidence of off-target probe binding affecting 10x Genomics Xenium gene panels compromise accuracy of spatial transcriptomic profiling.

eLife·2026
Same author

A reference genome sequence for the exceptionally long-lived Great Basin bristlecone pine, Pinus longaeva.

G3 (Bethesda, Md.)·2026

Related Experiment Video

Updated: Jul 18, 2025

Metagenomic Analysis of Silage
08:43

Metagenomic Analysis of Silage

Published on: January 13, 2017

18.4K

Metagenomic classification with KrakenUniq on low-memory computers.

Christopher Pockrandt1,2, Aleksey V Zimin1,2, Steven L Salzberg1,2,3,4

  • 1Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA.

Journal of Open Source Software
|August 21, 2023
PubMed
Summary

KrakenUniq now efficiently processes large metagenomic databases by loading them in chunks, not requiring excessive RAM. This makes high-accuracy sequence classification accessible on standard computers, even laptops.

More Related Videos

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
08:03

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Published on: December 7, 2021

2.2K
Evaluating the Impact of Hydraulic Fracturing on Streams using Microbial Molecular Signatures
09:11

Evaluating the Impact of Hydraulic Fracturing on Streams using Microbial Molecular Signatures

Published on: April 4, 2021

3.2K

Related Experiment Videos

Last Updated: Jul 18, 2025

Metagenomic Analysis of Silage
08:43

Metagenomic Analysis of Silage

Published on: January 13, 2017

18.4K
Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
08:03

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Published on: December 7, 2021

2.2K
Evaluating the Impact of Hydraulic Fracturing on Streams using Microbial Molecular Signatures
09:11

Evaluating the Impact of Hydraulic Fracturing on Streams using Microbial Molecular Signatures

Published on: April 4, 2021

3.2K

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Kraken and KrakenUniq are essential tools for metagenomic sequence classification.
  • Large databases (100-400 GB) are required, traditionally demanding significant RAM.
  • Previous versions suffered performance issues with insufficient RAM due to memory mapping.

Purpose of the Study:

  • To improve KrakenUniq's ability to handle large databases on systems with limited RAM.
  • To enhance the accessibility and efficiency of metagenomic analysis.

Main Methods:

  • Implemented a new algorithm in KrakenUniq for chunk-based database processing.
  • Optimized data loading and management to reduce memory footprint.

Main Results:

  • The enhanced KrakenUniq can process massive databases on standard hardware, including laptops.
  • Achieved a modest increase in running time compared to the significant slowdowns from memory mapping.
  • Maintained high classification accuracy.

Conclusions:

  • The new KrakenUniq algorithm democratizes high-performance metagenomic analysis.
  • Enables efficient use of KrakenUniq without requiring expensive high-memory servers.
  • Facilitates broader application in medical diagnostics, microbiome, and environmental studies.