ArticleG3 (Bethesda, Md.)2016
Suitability of Different Mapping Algorithms for Genome-Wide Polymorphism Scans with Pool-Seq Data.
Article in G3 (Bethesda, Md.), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
22 citing papers in PubMed, 44 citations in OpenAlex.
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- Comparative genomics of rainbow trout (Ecology and evolution · 2023Article
- Genome-wide selection signatures reveal widespread synergistic effects of two different stressors inProceedings. Biological sciences · 2022Article
- Genome-enabled discovery of candidate virulence loci in Striga hermonthica, a devastating parasite of African cereal crops.The New phytologist · 2022Article
- Slow Recovery from Inbreeding Depression Generated by the Complex Genetic Architecture of Segregating Deleterious Mutations.Molecular biology and evolution · 2022Article
- The genetic architecture of temperature adaptation is shaped by population ancestry and not by selection regime.Genome biology · 2021Article
- Evolutionary Genomics of Structural Variation in Asian Rice (Oryza sativa) Domestication.Molecular biology and evolution · 2020Article
- Fitness effects for Ace insecticide resistance mutations are determined by ambient temperature.BMC biology · 2020Article
- Multi-model seascape genomics identifies distinct environmental drivers of selection among sympatric marine species.BMC evolutionary biology · 2020Article
- Secondary Evolve and Resequencing: An Experimental Confirmation of Putative Selection Targets without Phenotyping.Genome biology and evolution · 2020Article
- Long-Term Dynamics AmongFrontiers in genetics · 2020Article
- Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast.Science advances · 2019Article
- Exploring a Pool-seq-only approach for gaining population genomic insights in nonmodel species.Ecology and evolution · 2019Article
- Origin and Consequences of Chromosomal Inversions in the virilis Group of Drosophila.Genome biology and evolution · 2018Article
- A simple genetic basis of adaptation to a novel thermal environment results in complex metabolic rewiring in Drosophila.Genome biology · 2018Article
- Phosphorylation State of ZFP24 Controls Oligodendrocyte Differentiation.Cell reports · 2018Article
- Complex signatures of genomic variation of two non-model marine species in a homogeneous environment.BMC genomics · 2018Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
The cost-effectiveness of sequencing pools of individuals (Pool-Seq) provides the basis for the popularity and widespread use of this method for many research questions, ranging from unraveling the genetic basis of complex traits, to the clonal evolution of cancer cells. Because the accuracy of Pool-Seq could be affected by many potential sources of error, several studies have determined, for example, the influence of sequencing technology, the library preparation protocol, and mapping parameters. Nevertheless, the impact of the mapping tools has not yet been evaluated. Using simulated and real Pool-Seq data, we demonstrate a substantial impact of the mapping tools, leading to characteristic false positives in genome-wide scans. The problem of false positives was particularly pronounced when data with different read lengths and insert sizes were compared. Out of 14 evaluated algorithms novoalign, bwa mem and clc4 are most suitable for mapping Pool-Seq data. Nevertheless, no single algorithm is sufficient for avoiding all false positives. We show that the intersection of the results of two mapping algorithms provides a simple, yet effective, strategy to eliminate false positives. We propose that the implementation of a consistent Pool-Seq bioinformatics pipeline, building on the recommendations of this study, can substantially increase the reliability of Pool-Seq results, in particular when libraries generated with different protocols are being compared.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.