Dataset Information

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

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.

SUBMITTER: Taron UH

PROVIDER: S-EPMC5867878 | biostudies-literature | 2018 Mar

REPOSITORIES: biostudies-literature

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

Taron Ulrike H UH Lell Moritz M Barlow Axel A Paijmans Johanna L A JLA

Genes 20180313 3

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 hig ...[more]

PMID: 29533977

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Project description:In implant dentistry, the advent of intraoral scanning technology has revolutionized traditional clinical processes by streamlining procedures and ensuring predictable treatment outcomes. However, achieving accurate virtual implant positions using intraoral scanners and scan bodies can be influenced by various clinical and laboratory factors. This study aims to investigate the impact of scan body image capture deficiency and scan body alignment methods in computer-aided design (CAD) software on the accuracy of virtual implant positions, particularly in different implant depths. Three stereolithographic half-arch implant models with different implant depths were prepared, representing three scenarios of scan body exposure: full exposed scan body, 2/3 exposed scan body, and 1/3 exposed scan body. The scan body image capture deficiency and alignment methods were simulated using CAD software. The deviation of virtual implant positions obtained from different scenarios were evaluated using 3D analysis software. The highest angular and linear deviation (0.237±0.059 degrees, 0.084±0.068 mm) were found in the 1/4 upper and lower part scan body deficiency using the 1-point alignment method in the 1/3 exposed scan body. Two-way ANOVA analysis revealed significant effects of scan deficiency on virtual implant position deviations across all scan body exposures, except for the linear deviation when the scan body was exposed 2/3 of its length. Furthermore, scan deficiencies in the 1/4 upper and lower parts of the scan body significantly affected implant angular deviation regardless of scan body exposure, while implant linear deviation was specifically affected when the scan body was exposed to only 1/3 of its total length. Deficiencies in scan body acquisition, particularly in deep soft tissue situations, can lead to deviations in both angular and linear positioning of virtual implants. Employing appropriate scan body alignment methods such as a 3-point alignment approach demonstrates better accuracy compared to a 1-point alignment.

Dataset Information

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

Publications

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

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