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NgsRelate: a software tool for estimating pairwise relatedness from next-generation sequencing data

Thorfinn Sand Korneliussen, Ida Moltke
2015 Bioinformatics  
Results: We present a software tool, NgsRelate, for estimating pairwise relatedness from NGS data.  ...  However, all existing estimation methods are based on called genotypes, which is not ideal for next-generation sequencing (NGS) data of low depth from which genotypes cannot be called with high certainty  ...  Motivated by this we developed NgsRelate; a ML method for estimating the pairwise relatedness parameter R from NGS data based on GLs.  ... 
doi:10.1093/bioinformatics/btv509 pmid:26323718 pmcid:PMC4673978 fatcat:bu6ombrxczgjrlu4sg273tigmm

NGSremix: A software tool for estimating pairwise relatedness between admixed individuals from next-generation sequencing data [article]

Anne Krogh Nøhr, Kristian Hanghøj, Genis Garcia Erill, Ida Moltke, Anders Albrechtsen
2020 bioRxiv   pre-print
However, the methods that can account for admixture are all based on genotype data as input, which is a problem for low depth next-generation sequencing (NGS) data from which genotypes are called with  ...  Hence, NGSremix is a useful new tool for estimating relatedness in admixed populations from low-depth NGS data.  ...  Discussion We have presented a new maximum likelihood based software tool, NGSremix, for estimation of pairwise relatedness between admixed individuals sequenced at low depth.  ... 
doi:10.1101/2020.10.20.347500 fatcat:usn3smpnjze2fogaimf2qox67i

NGSremix: A software tool for estimating pairwise relatedness between admixed individuals from next-generation sequencing data

Anne Krogh Nøhr, Kristian Hanghøj, Genis Garcia Erill, Zilong Li, Ida Moltke, Anders Albrechtsen
2021 G3: Genes, Genomes, Genetics  
However, the methods that can account for admixture are all based on genotype data as input, which is a problem for low-depth next-generation sequencing (NGS) data from which genotypes are called with  ...  Hence, NGSremix is a useful new tool for estimating relatedness in admixed populations from low-depth NGS data.  ...  DISCUSSION We have presented a new maximum likelihood based software tool, NGSremix, for estimation of pairwise relatedness between admixed individuals sequenced at low depth.  ... 
doi:10.1093/g3journal/jkab174 pmid:34015083 pmcid:PMC8496226 fatcat:66frcehrd5e4najlub4umpyr6m

The Identification of a 1916 Irish Rebel: New Approach for Estimating Relatedness From Low Coverage Homozygous Genomes

Daniel Fernandes, Kendra Sirak, Mario Novak, John A. Finarelli, John Byrne, Edward Connolly, Jeanette E. L. Carlsson, Edmondo Ferretti, Ron Pinhasi, Jens Carlsson
2017 Scientific Reports  
with the onset of Next Generation Sequencing (NGS) just over one decade ago.  ...  Next-generation shotgun sequencing has enabled aDNA studies to progress at a much faster rate than before, and when applied in  ...  Sudipto Das for his comments on sequencing methods; Dr. Eppie Jones for comments on the manuscript; the Irish Government for their support throughout the Thomas Kent identification process; and Dr.  ... 
doi:10.1038/srep41529 pmid:28134350 pmcid:PMC5278401 fatcat:dtm3vpgr3rd3dfzncehenj3cvq

Fast and accurate relatedness estimation from high-throughput sequencing data in the presence of inbreeding

Kristian Hanghøj, Ida Moltke, Philip Alstrup Andersen, Andrea Manica, Thorfinn Sand Korneliussen
2019 GigaScience  
The estimation of relatedness between pairs of possibly inbred individuals from high-throughput sequencing (HTS) data has previously not been possible for samples where we cannot obtain reliable genotype  ...  calls, as in the case of low-coverage data.  ...  Acknowledgements We thank the reviewers for their helpful comments.  ... 
doi:10.1093/gigascience/giz034 pmid:31042285 pmcid:PMC6488770 fatcat:odw6hrzswfdlxoc7sumqkanwoy

How a Paleogenomic Approach Can Provide Details on Bioarchaeological Reconstruction: A Case Study from the Globular Amphorae Culture

Stefania Vai, Maria Angela Diroma, Costanza Cannariato, Alicja Budnik, Martina Lari, David Caramelli, Elena Pilli
2021 Genes  
In this study, mitochondrial and nuclear genome data obtained from human bone remains associated with the Neolithic Globular Amphorae culture, which were recovered in the Megalithic barrow of Kierzkowo  ...  Due to its characteristics, the study of the Kierzkowo barrow represented a challenge for the reconstruction of the biological profile of the human community who exploited it and an excellent example of  ...  Data Availability Statement: The data analysed in this study are openly available in the European Nucleotide Archive (ENA) under accession numbers ERS2040835-ERS2040840, ERS2040844, and ERS2040845.  ... 
doi:10.3390/genes12060910 pmid:34208224 pmcid:PMC8230892 fatcat:3yzaq7ofkjfvzjxthak5difngq

TKGWV2: An ancient DNA relatedness pipeline for ultra-low coverage whole genome shotgun data [article]

Daniel M Fernandes, Olivia Cheronet, Pere Gelabert, Ron Pinhasi
2021 bioRxiv   pre-print
Although a few different methods have been specifically developed for ancient DNA, namely to tackle issues such as low-coverage homozygous data, they require a 0.1 - 1x minimum average genomic coverage  ...  In recent years, the numbers of sequenced individuals from single sites have been increasing, reflecting a growing interest in understanding the familial and social organisation of ancient populations.  ...  Mittnik for discussions before submission.  ... 
doi:10.1101/2021.06.22.449449 fatcat:2fcao5jqerekblosjjydzfjbfa

A genomic snapshot of demographic and cultural dynamism in Upper Mesopotamia during the Neolithic Transition [article]

N. Ezgi Altinisik, Duygu Deniz Kazanci, Ayca Aydogan, Hasan Can Gemici, Omur Dilek Erdal, Savas Sarialtun, Kivilcim Basak Vural, Dilek Koptekin, Kanat Gurun, Ekin Saglican, Gokhan Cakan, Meliha Melis Koruyucu (+12 others)
2022 bioRxiv   pre-print
We present thirteen ancient genomes (c.8500-7500 calBCE) from Pre-Pottery Neolithic Çayönü in the Tigris basin together with bioarchaeological and material culture data.  ...  Our findings reveal that Çayönü was a genetically diverse population, carrying a mixed ancestry from western and eastern Fertile Crescent, and that the community received immigrants.  ...  and SNIC/Uppsala Multidisciplinary Center for Advanced Computational Science for assistance with massively parallel sequencing and access to the UPPMAX computational infrastructure.  ... 
doi:10.1101/2022.01.31.478487 fatcat:i5zr6vzdbndbteq2yqatbfbamm

A 90K SNP array uncovers inbreeding and cryptic relatedness in an Antarctic fur seal breeding colony [article]

Emily Humble, Anneke J Paijmans, Jaume Forcada, Joseph I Hoffman
2020 biorxiv/medrxiv   pre-print
Overall, our SNP array will facilitate future studies of Antarctic fur seals and has the potential to serve as a more general resource for the wider pinniped research community.  ...  SNPs were discovered from a combination of genomic and transcriptomic resources and filtered according to strict criteria.  ...  Samples were collected as part of the Polar Science for Planet  ... 
doi:10.1101/2020.04.01.020123 fatcat:7oaumzm5jzamfe4ykfqedsdryq

Identifying a living great-grandson of the Lakota Sioux leader Tatanka Iyotake (Sitting Bull)

Ida Moltke, Thorfinn Sand Korneliussen, Andaine Seguin-Orlando, J. Víctor Moreno-Mayar, Ernie LaPointe, William Billeck, Eske Willerslev
2021 Science Advances  
E.L. helped collect the saliva samples from the Lakota Sioux individuals and provided access to Sitting Bull's hair  ...  T.S.K. was funded by a Carlsberg Foundation Young Researcher Fellowship awarded by the Carlsberg Foundation in 2019 (CF19-0712). Author contributions: E.W. initiated and led the study.  ...  (32) implemented in ANGSD (Analysis of Next Generation Sequencing Data) (33) to estimate base type-specific error rates for sequencing data from the Sitting Bull hair sample.  ... 
doi:10.1126/sciadv.abh2013 pmid:34705496 pmcid:PMC8550246 fatcat:uteo3am3tfdc5hxwzj46lpvn34

An overview of current population genomics methods for the analysis of whole-genome resequencing data in eukaryotes

Yann X C Bourgeois, Ben H Warren
2021 Molecular Ecology  
The constant improvement of high-throughput sequencing techniques has facilitated the production of whole genome data in a wide range of species.  ...  However, this improvement has come with a profusion of analytical tools that can confuse and discourage users.  ...  We also thank Gabriel Renaud and Peter Ralph for suggesting additional methods. AUTH O R CO NTR I B UTI O N YB wrote the first draft of the manuscript and maintained the website.  ... 
doi:10.1111/mec.15989 pmid:34009688 fatcat:q5ctfy5uvzbu7j24s26ai764me

An 85K SNP Array Uncovers Inbreeding and Cryptic Relatedness in an Antarctic Fur Seal Breeding Colony

Emily Humble, Anneke J. Paijmans, Jaume Forcada, Joseph I. Hoffman
2020 G3: Genes, Genomes, Genetics  
Overall, our SNP array will facilitate future studies of Antarctic fur seals and has the potential to serve as a more general resource for the wider pinniped research community.  ...  SNPs were discovered from a combination of genomic and transcriptomic resources and filtered according to strict criteria.  ...  The resulting genotype data were analyzed using Affymetrix Power Tools (APT) command line software.  ... 
doi:10.1534/g3.120.401268 pmid:32540866 pmcid:PMC7407454 fatcat:foqutp3reffjjhb6gng3o2yb2m

Physiological and Genetic Adaptations to Diving in Sea Nomads

Melissa A. Ilardo, Ida Moltke, Thorfinn S. Korneliussen, Jade Cheng, Aaron J. Stern, Fernando Racimo, Peter de Barros Damgaard, Martin Sikora, Andaine Seguin-Orlando, Simon Rasmussen, Inge C.L. van den Munckhof, Rob ter Horst (+5 others)
2018 Cell  
d We find evidence of additional diving-related phenotypes under selection d These findings have implications for hypoxia research, a pertinent medical issue  ...  Graphical Abstract Highlights d The Bajau, or "Sea Nomads," have engaged in breath-hold diving for thousands of years d Selection has increased Bajau spleen size, providing an oxygen reservoir for diving  ...  We would also like to acknowledge GenomeDK HPC Hub at Aarhus University and its staff, the staff of the Danish National High-throughput DNA Sequencing Centre, the laboratory technicians of the Centre for  ... 
doi:10.1016/j.cell.2018.03.054 pmid:29677510 fatcat:ntjiqtzrzrfbrew4jtzchobvg4

The Last Two Remaining Populations of the Critically Endangered Estuarine Pipefish Are Inbred and Not Genetically Distinct

Sven-Erick Weiss, Arsalan Emami-Khoyi, Horst Kaiser, Paul D. Cowley, Nicola C. James, Bettine Jansen van Vuuren, Alan K. Whitfield, Peter R. Teske
2022 Frontiers in Marine Science  
Here, we genotyped 34 pipefish from both populations using genome-wide data to determine whether the two estuaries harbour distinct genetic diversity, such that translocating individuals between them might  ...  Even though recent surveys have estimated population sizes in the order of thousands of individuals, these may fluctuate considerably.  ...  A., Manica, A., and Korneliussen, T. S. (2019). Fast and accurate relatedness estimation from high-throughput sequencing data in the presence of inbreeding.  ... 
doi:10.3389/fmars.2021.756595 fatcat:yrcsavfvmnc4boqpe6uu3riz7u

The Discovery of Wild Date Palms in Oman Reveals a Complex Domestication History Involving Centers in the Middle East and Africa

Muriel Gros-Balthazard, Marco Galimberti, Athanasios Kousathanas, Claire Newton, Sarah Ivorra, Laure Paradis, Yves Vigouroux, Robert Carter, Margareta Tengberg, Vincent Battesti, Sylvain Santoni, Laurent Falquet (+3 others)
2017 Current Biology  
For many crops, wild relatives constitute an extraordinary resource for cultivar improvement [1, 2] and also help to better understand the history of their domestication [3] .  ...  We acknowledge Tosso Leeb for assistance in library preparation and sequencing; Megan Bowman, Ning Jiang, Katharina Hoff, and Carson Holt for their support in establishing the gene annotation pipeline;  ...  issuing permissions for this study.  ... 
doi:10.1016/j.cub.2017.06.045 pmid:28712568 fatcat:4h5yvcvi3ved3nwwqwvyyqeebi
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