Quick Analysis of Sedimentary Ancient DNA Using quicksand

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.