ArticleGenes2018
Testing of Alignment Parameters for Ancient Samples: Evaluating and Optimizing Mapping Parameters for Ancient Samples Using the TAPAS Tool.
Article in Genes, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- The origins and diversification of Holarctic brown bear populations inferred from genomes of past and present populations.Proceedings. Biological sciences · 2024Article
- An extinct and deeply divergent tiger lineage from northeastern China recognized through palaeogenomics.Proceedings. Biological sciences · 2022Article
- Diversity and Paleodemography of the Addax (Genes · 2021Article
- Recovery and analysis of ancient beetle DNA from subfossil packrat middens using high-throughput sequencing.Scientific reports · 2021Article
- Identifying the true number of specimens of the extinct blue antelope (Hippotragus leucophaeus).Scientific reports · 2021Article
- Ancient DNA from the Asiatic Wild Dog (Genes · 2021Article
- Metagenomic analysis of a blood stain from the French revolutionary Jean-Paul Marat (1743-1793).Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2020Article
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- Article
- Paleogenomics: reconstruction of plant evolutionary trajectories from modern and ancient DNA.Genome biology · 2019Article
- Metagenomic Composition Analysis of an Ancient Sequenced Polar Bear Jawbone from Svalbard.Genes · 2018Article
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4 authors.
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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 (
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