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Dataset results
20 results for “reading impact”
Variant calling in the Goldilocks Zone: how reference genome choice and read mapping stringency impact heterozygosity estimates and phylogenetic analyses
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Supplementary materials for: Exploring the impact of read clustering thresholds on RADseq-based systematics: an empirical example from European amphibians
<p><span>Restriction site-Associated DNA sequencing (RADseq) has great potential for genome-wide systematics studies of non-model organisms. However, accurately assembling RADseq reads into orthologous loci remains a major challenge in the absence of a reference genome. Traditional assembly pipelines cluster putative orthologous sequences based on a user-defined clustering threshold. Because improper clustering of orthologs is expected to affect results in downstream analyses, it is crucial to design pipelines for empirically optimizing the clustering threshold. While this issue has been largely discussed from a population genomics perspective, it remains understudied in the context of phylogenomics and coalescent species delimitation. To address this issue, we generated RADseq assemblies of representatives of the amphibian genera <em>Discoglossus</em>, <em>Rana</em>, <em>Lissotriton</em> and <em>Triturus</em> using a wide range of clustering thresholds. Particularly, we studied the effects of the intra-sample Clustering Threshold (iCT) and between-sample Clustering Threshold (bCT) separately, as both are expected to differ in multi-species data sets. The obtained assemblies were used for downstream inference of concatenation-based phylogenies, and multi-species coalescent species trees and species delimitation. The results were evaluated in the light of a reference genome-wide phylogeny calculated from newly generated Hybrid-Enrichment markers, as well as extensive background knowledge on the species' systematics. Overall, our analyses show that the inferred topologies and their resolution are resilient to changes of the iCT and bCT, regardless of the analytical method employed. Except for some extreme clustering thresholds, all assemblies yielded identical, well-supported inter-species relationships that were mostly congruent with those inferred from the reference Hybrid-Enrichment data set. Similarly, coalescent species delimitation was consistent among similarity threshold values. However, we identified a strong effect of the bCT on the branch lengths of concatenation and species trees, with higher bCTs yielding trees with shorter branches, which might be a pitfall for downstream inferences of evolutionary rates. Our results suggest that the choice of assembly parameters for RADseq data in the context of shallow phylogenomics might be less challenging than previously thought. Finally, we propose a pipeline for empirical optimization of the iCT and bCT, implemented in optiRADCT, a series of scripts readily usable for future RADseq studies.</span></p>
Supplementary materials for: Exploring the impact of read clustering thresholds on RADseq-based systematics: an empirical example from European amphibians
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The impact of contaminants on the accuracy of genome skimming and the effectiveness of exclusion read filters
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Data from: Structural variation and its potential impact on genome instability: novel discoveries in the EGFR landscape by long-read sequencing
<p>Studies of structural variation (SV) have been challenging due to technological contraints. With the advent of third generation (long-read) sequencing technology, exploration of longer stretches of DNA not easily examined previously has been made possible. In the present study, we utilized third generation (long-read) sequencing techniques to examime SV in the <em>EGFR </em>landscape of four haplotypes derived from two human samples. We analyzed the <em>EGFR</em> gene and its landscape (+/- 500,000 base pairs) using this sequencing approach and were able to identify regions of non-coding DNA which had relatively high similarity to the most common activating <em>EGFR</em> mutation in non-small cell lung cancer. We discovered that reverse complements to the exon 19 deletion mutation which had at least 60% homology to the <em>EGFR</em> exon 19 canonical deletion and were within ± 421,000 bp of the deletion varied across the five haploid genomes examined (4 patient landscapes and hg38). Although the sample size is limited in this study, the estimated variation observed in genomic stability between the five <em>EGFR</em> haplotypes examined is novel and encourages further work to examine structural variation in larger cohorts.</p>
Data from: Exploring the impact of read clustering thresholds on RADseq-based systematics: an empirical example from European amphibians.
<p>This repository contains genetic sequences obtained from Hybrid-Enrichment and RAD sequencing protocols of the amphibian genera <em>Discoglossus</em>, <em>Lissotriton</em>, <em>Rana </em>and <em>Triturus, </em>as well as phylogenetic trees inferred from the RADseq data. This data was generated for the manuscript "Exploring the impact of read clustering thresholds on RADseq-based systematics: an empirical example from European amphibians.", in which we tested the influence of the clustering threshold used to assemble RADseq data on downstream phylogenetic inferences. Details on the data generation and analyses can be found in the manuscript and related supplementary materials.</p> <p>The repository is organised as follow:</p> <p>-> Hybrid-Enrichment: alignments of the Hybrid-Enrichment markers in phylip/fasta format (with one subdirectory for each of the four datasets assembled: Discoglossus, Lissotriton, Rana, Triturus)</p> <p>--> RADseq: Assemblies and phylogenetic trees obtained from a RADseq protocol</p> <p> --> Assemblies: RADseq assemblies (complete loci sequences and SNP matrices, spreadsheets with assembly metrics). Divided into "iCT" (assemblies produced with 23 different intra-sample Clustering Threshold [iCT] and a fixed between-samples Clustering Threshold [bCT]) and "bCT" (assemblies produced with a fixed iCT and 23 different bCT). Both iCT and bCT are further divided in four sub-directories corresponding to the four datasets: Discoglossus, Lissotriton, Rana, Triturus)</p> <p> --> Trees: Phylogenetic trees inferred from the aforementionned assemblies. Divided into "iCT" (RAxML concatenation trees inferred from the assemblies with different iCTs) and "bCT" (RAxML concatenation trees and Tetrad species trees inferred from the assemblies with different bCTs).</p>
Impact of Reading on Endogenous Oxytocin System of Preterm Infants
ClinicalTrials.gov study NCT05412524. IPD Sharing: NO. Countries: 1. Publications: 5.
Rhythm Training of a Serious Game on the Reading Skills of Children w/ a Specific Learning Disorder Impacting Reading
ClinicalTrials.gov study NCT05154721. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Impact of Motor Tasks and Lidocaine on Reading Unfamiliar Words in Adults With and Without Dyslexia
ClinicalTrials.gov study NCT05854082. IPD Sharing: NO. Countries: 1. Publications: 0.
Data from: Structural variation and its potential impact on genome instability: novel discoveries in the EGFR landscape by long-read sequencing
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ENHANCING READING SKILLS AMONG HIGH SCHOOL PUPILS: STRATEGIES AND IMPACT
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INTEGRATION AND IMPACT OF AI AND COLLABORATIVE TECHNOLOGIES ON READING SKILL DEVELOPMENT
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Evaluation of the Potential Impact of an Artificial Intelligence Solution in Second Reading of Organized Screening.
ClinicalTrials.gov study NCT06479772. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Impact of Narrative Medicine (Workshop Reading Diaries)
ClinicalTrials.gov study NCT01798290. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Impact of Picture Book Reading on Preterm Infant Stability, Parental Anxiety, and Parent-Child Attachment
ClinicalTrials.gov study NCT06854549. IPD Sharing: NO. Countries: 1. Publications: 0.
Impact of the "Kid'EM App" Digital Guidance Tool for Setting Rehabilitation Goals by the Rehabilitation Professional for Children with Chronic Conditions Impacting Physical Health (READ'APP'T)
ClinicalTrials.gov study NCT06475950. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.
Pilot for a Community Pharmacy Service Model: Impact of a Pharmacist Monitored Patient Blood Pressure Readings
ClinicalTrials.gov study NCT03323840. IPD Sharing: NO. Countries: 1. Publications: 0.
Impact of a Double-reading Animated Film (Child, Parents) in Preoperative on the Anxiety of Children Upon Arrival at the Operating Room
ClinicalTrials.gov study NCT04252508. IPD Sharing: NO. Countries: 1. Publications: 0.
Impact of Free Reading Glasses on Work and Visual Function Following Cataract Surgery in Honduras
ClinicalTrials.gov study NCT06136780. IPD Sharing: YES. Countries: 0. Publications: 0.
The Impact of Shallow Reading in Social Media
ClinicalTrials.gov study NCT05097807. IPD Sharing: YES. Countries: 0. Publications: 0.
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OpenNeuro
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