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Related Experiment Video

Updated: Jan 10, 2026

Extraction of High Molecular Weight Genomic DNA from Soils and Sediments

Extraction of High Molecular Weight Genomic DNA from Soils and Sediments

Published on: November 10, 2009

Quick Analysis of Sedimentary Ancient DNA Using quicksand.

Merlin Szymanski¹, Johann Visagie¹, Frederic Romagne¹

¹Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.

Molecular Biology and Evolution

|November 25, 2025

Summary

This summary is machine-generated.

We developed quicksand, a computational pipeline for analyzing ancient environmental DNA (sedaDNA). This tool rapidly and accurately identifies mammalian species from sediment samples, improving archaeological research.

Keywords:

ancient DNA archaeology bioinformatics genomics sedaDNA

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Last Updated: Jan 10, 2026

Extraction of High Molecular Weight Genomic DNA from Soils and Sediments

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Published on: November 10, 2009

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Optimized Bone Sampling Protocols for the Retrieval of Ancient DNA from Archaeological Remains

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Published on: November 30, 2021

Area of Science:

Paleogenomics
Bioinformatics
Archaeological Science

Background:

Ancient DNA from sediments (sedaDNA) offers insights into past ecosystems and human activities.
Computational challenges exist in classifying large sedaDNA sequencing datasets, particularly regarding speed and accuracy.
Current alignment-based methods are slow, while alignment-free methods have higher error rates.

Purpose of the Study:

To develop an efficient and accurate computational pipeline for taxonomic classification of mammalian mitochondrial DNA in sedaDNA.
To address the limitations of existing sedaDNA analysis tools, balancing speed and accuracy.

Main Methods:

Developed quicksand, an open-source Nextflow pipeline.
Integrated fast alignment-free classification (KrakenUniq) with post-classification mapping and filtering.
Included ancient DNA authentication steps.

Main Results:

quicksand achieves high accuracy and sensitivity in taxonomic classification of mammalian mitochondrial DNA.
The pipeline significantly reduces computational runtime compared to existing methods.
Demonstrated comparable or superior performance to current standards via simulations and reanalysis of published data.

Conclusions:

quicksand provides a rapid and accurate solution for sedaDNA taxonomic classification.
The pipeline facilitates large-scale screening of sedaDNA samples for archaeological research.
Offers an accessible workflow for analyzing ancient environmental DNA data.