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Genes 2018, 9(3), 157; https://doi.org/10.3390/genes9030157

Testing of Alignment Parameters for Ancient Samples: Evaluating and Optimizing Mapping Parameters for Ancient Samples Using the TAPAS Tool

Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
These authors contributed equally to this work.
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Received: 20 December 2017 / Revised: 6 March 2018 / Accepted: 8 March 2018 / Published: 13 March 2018
(This article belongs to the Special Issue Novel and Neglected Areas of Ancient DNA Research)
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Abstract

High-throughput sequence data retrieved from ancient or other degraded samples has led to unprecedented insights into the evolutionary history of many species, but the analysis of such sequences also poses specific computational challenges. The most commonly used approach involves mapping sequence reads to a reference genome. However, this process becomes increasingly challenging with an elevated genetic distance between target and reference or with the presence of contaminant sequences with high sequence similarity to the target species. The evaluation and testing of mapping efficiency and stringency are thus paramount for the reliable identification and analysis of ancient sequences. In this paper, we present ‘TAPAS’, (Testing of Alignment Parameters for Ancient Samples), a computational tool that enables the systematic testing of mapping tools for ancient data by simulating sequence data reflecting the properties of an ancient dataset and performing test runs using the mapping software and parameter settings of interest. We showcase TAPAS by using it to assess and improve mapping strategy for a degraded sample from a banded linsang (Prionodon linsang), for which no closely related reference is currently available. This enables a 1.8-fold increase of the number of mapped reads without sacrificing mapping specificity. The increase of mapped reads effectively reduces the need for additional sequencing, thus making more economical use of time, resources, and sample material. View Full-Text
Keywords: ancient DNA; short-read mapping; palaeogenomics; paleogenomics; alignment sensitivity/specificity ancient DNA; short-read mapping; palaeogenomics; paleogenomics; alignment sensitivity/specificity
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Taron, U.H.; Lell, M.; Barlow, A.; Paijmans, J.L.A. Testing of Alignment Parameters for Ancient Samples: Evaluating and Optimizing Mapping Parameters for Ancient Samples Using the TAPAS Tool. Genes 2018, 9, 157.

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