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

Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

548
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...
548
Applications of Molecular Taxonomy01:20

Applications of Molecular Taxonomy

480
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...
480

You might also read

Related Articles

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

Sort by
Same author

Ultra-accurate sequencing reveals an extreme transmission bottleneck in a deep-sea clam symbiosis.

bioRxiv : the preprint server for biology·2026
Same author

Is Arthroscopic Disc Repositioning Associated With Condylar Height Change in Adolescents and Young Adults With Anterior Disc Displacement Without Reduction?

Journal of oral and maxillofacial surgery : official journal of the American Association of Oral and Maxillofacial Surgeons·2026
Same author

EMS mutation and SNP detection in intracellular <i>Wolbachia</i> genomes.

mSystems·2026
Same author

Interactive exploration of biobank-scale ancestral recombination graphs with Lorax.

Bioinformatics (Oxford, England)·2026
Same author

Splicing deficiency is driven by genomic erosion in non-recombining algal mating-type chromosomes.

PLoS biology·2026
Same author

Lethal plague outbreaks in Lake Baikal hunter-gatherers 5,500 years ago.

Nature·2026

Related Experiment Video

Updated: Jan 9, 2026

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing
11:22

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing

Published on: October 15, 2019

31.0K

Bamdam: a post-mapping authentication toolkit for ancient metagenomics.

Bianca De Sanctis1,2,3, Cade Mirchandani4,5, Haoran Dong6,7

  • 1Genomics Institute, University of California Santa Cruz, Santa Cruz, USA. bddesanctis@gmail.com.

Genome Biology
|December 5, 2025
PubMed
Summary
This summary is machine-generated.

This study introduces bamdam, a new toolkit for ancient DNA analysis. It efficiently processes metagenomic data, enhancing taxonomic identification and data integrity checks for microbial and eukaryotic studies.

Keywords:
Ancient DNAAuthenticationEnvironmental DNAMetagenomicsRead complexity

More Related Videos

DamID-seq: Genome-wide Mapping of Protein-DNA Interactions by High Throughput Sequencing of Adenine-methylated DNA Fragments
09:14

DamID-seq: Genome-wide Mapping of Protein-DNA Interactions by High Throughput Sequencing of Adenine-methylated DNA Fragments

Published on: January 27, 2016

20.0K
Investigating Bacterial-Fungal Interactions using Fungal Highway Columns in Diverse Environments and Substrates
05:22

Investigating Bacterial-Fungal Interactions using Fungal Highway Columns in Diverse Environments and Substrates

Published on: January 24, 2025

709

Related Experiment Videos

Last Updated: Jan 9, 2026

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing
11:22

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing

Published on: October 15, 2019

31.0K
DamID-seq: Genome-wide Mapping of Protein-DNA Interactions by High Throughput Sequencing of Adenine-methylated DNA Fragments
09:14

DamID-seq: Genome-wide Mapping of Protein-DNA Interactions by High Throughput Sequencing of Adenine-methylated DNA Fragments

Published on: January 27, 2016

20.0K
Investigating Bacterial-Fungal Interactions using Fungal Highway Columns in Diverse Environments and Substrates
05:22

Investigating Bacterial-Fungal Interactions using Fungal Highway Columns in Diverse Environments and Substrates

Published on: January 24, 2025

709

Area of Science:

  • Ancient DNA research
  • Metagenomics
  • Bioinformatics

Background:

  • Ancient metagenomic studies typically use pairwise read alignment and lowest common ancestor (LCA) assignment for taxonomic identification.
  • Existing methods can result in large data files and may not fully capture data authenticity.

Purpose of the Study:

  • To develop a lightweight toolkit, bamdam, for post-mapping and post-LCA analysis in eukaryotic and microbial metagenomics.
  • To improve the efficiency of processing ancient DNA data and enhance the reliability of taxonomic assignments.

Main Methods:

  • Developed bamdam, a toolkit that operates after initial read mapping and LCA assignment.
  • Implemented data compression techniques to significantly reduce the size of metagenomic BAM files.
  • Integrated computation of authentication metrics such as k-mer duplicity, postmortem damage, and mean read complexity.
  • Incorporated visualization tools, including deamination plots and interactive Krona plots colored by damage.

Main Results:

  • Bamdam effectively shrinks large metagenomic BAM files by a factor of 10x or more while preserving essential read and alignment information.
  • The toolkit computes a comprehensive suite of authentication metrics for taxonomic nodes, aiding in data quality assessment.
  • Generated advanced visualizations that facilitate the interpretation of multi-sample deamination patterns and damage distribution.

Conclusions:

  • Bamdam offers an efficient and robust solution for analyzing ancient metagenomic data.
  • The toolkit enhances data integrity through advanced authentication metrics and informative visualizations.
  • Bamdam is valuable for both microbial and eukaryotic ancient DNA research, improving taxonomic resolution and data quality control.