Testing of alignment parameters for ancient samples: evaluating and optimizing mapping parameters for ancient samples using the TAPAS tool

Taron, U., Lell, M., Barlow, A. ORCID: 0000-0002-5532-9458 and Paijmans, J., 2018. Testing of alignment parameters for ancient samples: evaluating and optimizing mapping parameters for ancient samples using the TAPAS tool. Genes, 9. ISSN 2073-4425

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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.

Item Type: Journal article
Publication Title: Genes
Creators: Taron, U., Lell, M., Barlow, A. and Paijmans, J.
Publisher: MDPI
Date: 13 March 2018
Volume: 9
ISSN: 2073-4425
Identifiers:
NumberType
10.3390/genes9030157DOI
1238796Other
Rights: © 2018 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
Divisions: Schools > School of Science and Technology
Depositing User: Jonathan Gallacher
Date Added: 05 Dec 2019 10:56
Last Modified: 05 Dec 2019 10:56
URI: http://irep.ntu.ac.uk/id/eprint/38759

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