Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
6
datasets available to search
ShareScore release 0.9.0
Dataset results
6 results for “Local ancestry”
Versatile simulations of admixture and accurate local ancestry inference with mixnmatch and ancestryinfer
It is now clear that hybridization between species is much more common than previously recognized. As a result, we now know that the genomes of many modern species, including our own, are a patchwork of regions derived from past hybridization events. Increasingly researchers are interested in disentangling which regions of the genome originated from each parental species using local ancestry inference methods. Due to the diverse effects of admixture, this interest is shared across disparate fields, from human genetics to research in ecology and evolutionary biology. However, local ancestry inference methods are sensitive to a range of biological and technical parameters which can impact accuracy. Here we present paired simulation and ancestry inference pipelines, mixnmatch and ancestryinfer, to help researchers plan and execute local ancestry inference studies. mixnmatch can simulate arbitrarily complex demographic histories in the parental and hybrid populations, selection on hybrids, and technical variables such as coverage and contamination. ancestryinfer takes as input sequencing reads from simulated or real individuals, and implements an efficient local ancestry inference pipeline. We perform a series of simulations with mixnmatch to pinpoint factors that influence accuracy in local ancestry inference and highlight useful features of the two pipelines. Together, mixnmatch and ancestryinfer are powerful tools for predicting the performance of local ancestry inference methods on real data.
Versatile simulations of admixture and accurate local ancestry inference with mixnmatch and ancestryinfer
Open the record for dataset details and reuse information.
Data from: Genome-wide local ancestry and the functional consequences of admixture in African and European cattle populations
Open the record for dataset details and reuse information.
Genomic Resources for Global and Local Ancestry Estimation in a Captive Baboon Colony
<p>VCF files mapped to <em>Panubis1.0</em> with 881 olive (<em>Papio anubis</em>) and yellow (<em>Papio cynocephalus</em>) baboons from the Southwest National Primate Research Center. VCF files were generated in two separate pipelines, first using Beagle 4.1 and Beagle 5.4 and additionally SHAPEIT5/IMPUTE5 to test if a pedigree-aware software reduced the number of evident phase switch errors. VCFs here have been phased and imputed in their respective pipelines, filtered for imputation accuracy with markers with less than 0.7 confidence removed using BCFTools, and then phase switch corrected using Tractor. Genomic resources (AIMs and Fixed markers) are based off of <em>Panubis1.0 </em>coordinates. Local ancestry estimation completed by RFMix and then phase-switch-corrected using Tractor. </p>
Local ancestry to identify selection in response to trypanosome infection in Baoulé x Zebu crossbred cattle in Burkina Faso
<p><span>The genomes of crossbred (admixed) individuals are a mosaic of ancestral haplotypes formed by recombination in each generation. The proportion of these ancestral haplotypes in certain genomic regions can be responsible for either susceptibility or resistance against pathogens, and for performances in production traits. Using dense genomic markers from the Illumina Bovine SNP50 BeadChip, we estimated individual admixture proportions for Baoulé x Zebu crossbred cattle in Burkina Faso, which were tested for trypanosome infection by direct ELISA from blood samples. Furthermore, we calculated local ancestry deviation from average for each SNP across 29 autosomes to identify potential regions under selection in the trypanotolerant Baoulé cattle and their crossbreds. We identified significant deviation from the local average ancestry (above 5% and 10% genome-wide thresholds) on chromosomes 8 and 19 in the positive animals, while the negative ones showed higher deviation on chromosomes 6, 19, 21 and 22. Screening for <i>F</i><sub>ST</sub> outliers in trypanosome positive/ negative animals we detected seven variants putatively under selection. Finally, we identified a minimum set of highly ancestry informative SNPs for routine admixture testing. Generally, results will serve as basis for further characterization, conservation and improvement strategies for purebred and crossbred populations. Our results are important not only for conserving the genetic integrity in the indigenous Baoulé cattle, but also for improving community-based breeding programs to increase trypanotolerance in crossbred populations.</span></p>
Local ancestry to identify selection in response to trypanosome infection in Baoulé x Zebu crossbred cattle in Burkina Faso
Open the record for dataset details and reuse information.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.