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Related Experiment Video

Updated: Feb 13, 2026

Optimized Bone Sampling Protocols for the Retrieval of Ancient DNA from Archaeological Remains
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Testing of Alignment Parameters for Ancient Samples: Evaluating and Optimizing Mapping Parameters for Ancient Samples

Ulrike H Taron1, Moritz Lell2, Axel Barlow

  • 1Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany. ulrike.taron@gmx.net.

Genes
|March 14, 2018
PubMed
Summary
This summary is machine-generated.

Ancient DNA analysis is challenging due to genetic distance and contamination. We developed TAPAS (Testing of Alignment Parameters for Ancient Samples) to optimize mapping strategies, increasing mapped reads by 1.8-fold for degraded samples.

Keywords:
alignment sensitivity/specificityancient DNApalaeogenomicspaleogenomicsshort-read mapping

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • High-throughput sequencing of ancient DNA provides evolutionary insights but presents computational challenges.
  • Mapping ancient sequence reads to reference genomes is difficult due to genetic distance and contaminants.
  • Evaluating mapping efficiency and stringency is crucial for reliable ancient sequence analysis.

Purpose of the Study:

  • To introduce TAPAS (Testing of Alignment Parameters for Ancient Samples), a computational tool for systematic testing of mapping tools for ancient DNA.
  • To simulate ancient DNA data properties and test various mapping software and parameters.
  • To improve mapping strategies for degraded samples lacking closely related references.

Main Methods:

  • Development of TAPAS, a computational tool for simulating ancient DNA datasets.
  • Systematic testing of mapping tools and parameter settings using simulated data.
  • Application of TAPAS to optimize mapping for a degraded banded linsang (Prionodon linsang) sample.

Main Results:

  • TAPAS enables systematic evaluation and optimization of alignment parameters for ancient DNA.
  • Improved mapping strategy for the banded linsang sample resulted in a 1.8-fold increase in mapped reads.
  • The increased mapped reads were achieved without compromising mapping specificity.

Conclusions:

  • TAPAS enhances the analysis of ancient and degraded DNA sequences.
  • Optimized mapping strategies reduce the need for extensive sequencing, saving resources.
  • The tool facilitates more economical and efficient use of time, resources, and precious sample material.