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ANGSD: Analysis of Next Generation Sequencing Data

Thorfinn Sand Korneliussen, Anders Albrechtsen, Rasmus Nielsen
2014 BMC Bioinformatics  
High-throughput DNA sequencing technologies are generating vast amounts of data.  ...  This program can calculate various summary statistics, and perform association mapping and population genetic analyses utilizing the full information in next generation sequencing data by working directly  ...  of analyses tools for ANGSD.  ... 
doi:10.1186/s12859-014-0356-4 pmid:25420514 pmcid:PMC4248462 fatcat:xujrgymmmrg2vhehih35egbc4q

ngsJulia: population genetic analysis of next-generation DNA sequencing data with Julia language

Alex Mas-Sandoval, Chenyu Jin, Marco Fracassetti, Matteo Fumagalli
2022 F1000Research  
A sound analysis of DNA sequencing data is important to extract meaningful information and infer quantities of interest.  ...  We further describe two implementations, ngsPool and ngsPloidy, for the analysis of pooled sequencing data and polyploid genomes, respectively.  ...  ngsPool: analysis of pooled sequencing data We used ngsJulia to implement a separate program, called ngsPool, to perform population genetic analysis from pooled sequencing data.  ... 
doi:10.12688/f1000research.104368.1 fatcat:j7w4irzdcjextgyx3c7mls6poa

ZAMS: A Pipeline for Accurate Variant Calling by Integrating Various Tools

Masum Billah
2019 Figshare  
Meaningful analysis of next-generation sequencing (NGS) data, extensively produced by genomics studies, relies largely on the accuracy and consistency of the genome variants and genotypes.  ...  Hence, a systematic comparison of the variant callers could give crucial outputs in any NGS-based genomics experiment.  ...  Next generation sequencing (NGS) platforms can generate large amounts of sequencing data, but often with high sequence error rates.  ... 
doi:10.6084/m9.figshare.7991618 fatcat:oodp7d3nevfpneyxb5c2gj6swe

ngsTools: methods for population genetics analyses from next-generation sequencing data

Matteo Fumagalli, Filipe G. Vieira, Tyler Linderoth, Rasmus Nielsen
2014 Computer applications in the biosciences : CABIOS  
Next-Generation Sequencing (NGS) technologies produce short reads that are either de novo assembled or mapped to a reference genome.  ...  However, for low sequencing depths, e.g. < 10×, there is considerable statistical uncertainty in the assignment of genotypes because of random sampling of homologous base pairs in heterozygotes, and sequencing  ...  ACKNOWLEDGEMENT We would like to thank Thorfinn Korneliussen and Anders Albrechtsen for helpful discussions and assistance using ANGSD.  ... 
doi:10.1093/bioinformatics/btu041 pmid:24458950 pmcid:PMC4016704 fatcat:3cemtmak3jdfrcaeksnbqcazuq

A Genotype Likelihood Framework for GWAS with Low Depth Sequencing Data from Admixed Individuals [article]

Emil Jørsboe, Anders Albrechtsen
2019 bioRxiv   pre-print
analysis.  ...  This makes it possible to properly account for genotype uncertainty in large scale association studies based on low depth sequencing data.  ...  However, a slightly different design is using low depth next-generation sequencing (NGS) data, because in such cases the genotype cannot be inferred accurately.  ... 
doi:10.1101/786384 fatcat:dn3m25bw65ekfmvy4fpxjtiex4

Mitochondrial DNA Consensus Calling and Quality Filtering for Constructing Ancient Human Mitogenomes: Comparison of Two Widely Applied Methods

Alexandros Heraclides, Eva Fernández-Domínguez
2022 International Journal of Molecular Sciences  
Raw genomic data (BAM/FASTQ) from a total of 17 previously published whole ancient human genomes ranging from the 14th to the 7th millennium BCE were retrieved and mitochondrial consensus sequences were  ...  Moreover, the influence of different sequence parameters (number of reads, sequenced bases, mean coverage, and rate of deamination and contamination) as predictors of derived sequence quality was evaluated  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/ijms23094651 pmid:35563041 pmcid:PMC9104972 fatcat:kjepfeanhfcvthtqm7rtoons2y

hapCon: Estimating contamination of ancient genomes by copying from reference haplotypes [article]

Yilei Huang, Harald Ringbauer
2021 bioRxiv   pre-print
We assessed an implementation of this new approach, hapCon, on simulated and down-sampled empirical aDNA data.  ...  We found that hapCon provides useful contamination estimates for coverages as low as 0.1x for SNP capture data (1240k) and 0.02x for whole genome sequencing data (WGS), substantially extending the coverage  ...  Acknowledgements We thank Yu He, Cosimo Posth and Johannes Krause for providing BAM files of hunter-gatherer samples prior to their publication.  ... 
doi:10.1101/2021.12.20.473429 fatcat:atntd5g7lng4lkncx5erofjytu

Population genomics in two cave-obligate invertebrates confirms extremely limited dispersal between caves

Andras Balogh, Lam Ngo, Kirk S. Zigler, Groves Dixon
2020 Scientific Reports  
Our results support the idea of caves as natural laboratories for the study of parallel evolutionary processes.  ...  Organisms that have evolved to exist under these pressures typically exhibit a suite of convergent characteristics, including a loss or reduction of eyes and pigmentation.  ...  Data analysis was performed with the help of the Texas Advanced Computing Center. We thank Mikhail Matz for support as well as assistance with analysis and composition.  ... 
doi:10.1038/s41598-020-74508-9 pmid:33067497 fatcat:2xwammvuh5g3xa6dp5hwof25nq

pixy: Unbiased estimation of nucleotide diversity and divergence in the presence of missing data [article]

Katharine L Korunes, Kieran Samuk
2020 bioRxiv   pre-print
Here, we address a widespread issue in π and dXY calculation: systematic bias generated by missing data of various types.  ...  unbiased estimates of π and dXY in the face of missing data.  ...  ANGSD relies on genotype 247 likelihoods calculated using the reads covering a position, making it incompatible with 248 our simulated data but equipped to handle empirical sequencing data. 249 250 All  ... 
doi:10.1101/2020.06.27.175091 fatcat:hdm4hsmpvfaujhwoxa62fjbulm

Supplementary Methods from A non-coding region near Follistatin controls head colour polymorphism in Gouldian finch

Matthew B. Toomey, Cristiana Marques, Pedro Andrade, Pedro M. Araújo, Stephen Sabatino, Małgorzata A. Gazda, Sandra Afonso, Ricardo J. Lopes, Joseph C. Corbo, Miguel Carneiro
2018 Figshare  
Korneliussen TS, Albrechtsen A, Nielsen R. 2014 ANGSD: Analysis of Next Generation Sequencing Data. BMC Bioinformatics 15, 356. (doi:10.1186/s12859-014-29.  ...  PLoS One 8, e79667. 365 366 367 368 369 370 next-generation sequencing data. Genetics 195, 979-992. 371 372 373 analysis of association studies.  ... 
doi:10.6084/m9.figshare.7091906.v1 fatcat:okq2rcovprd2lcqlenw4cchfhq

Fast and accurate estimation of multidimensional site frequency spectra from low-coverage high-throughput sequencing data

Alex Mas-Sandoval, Nathaniel S Pope, Knud Nor Nielsen, Isin Altinkaya, Matteo Fumagalli, Thorfinn Sand Korneliussen
2022 GigaScience  
number of populations, using low-coverage sequencing data.  ...  When applied to low-coverage sequencing data from the fungal pathogen Neonectria neomacrospora, results recapitulate the patterns of population differentiation generated using the original high-coverage  ...  Acknowledgements We thank the many users of the ANGSD suite who have provided useful feedback.  ... 
doi:10.1093/gigascience/giac032 pmid:35579549 pmcid:PMC9112775 fatcat:6mwmsmosyngjre33ysa54q63qa

High diversity, inbreeding and a dynamic Pleistocene demographic history revealed by African buffalo genomes

Deon de Jager, Brigitte Glanzmann, Marlo Möller, Eileen Hoal, Paul van Helden, Cindy Harper, Paulette Bloomer
2021 Scientific Reports  
Here, we produce 40 low coverage (7.14×) genome sequences of Cape buffalo (S. c. caffer) from four protected areas in South Africa.  ...  The results of this study have implications for buffalo management and conservation, particularly in the context of the predicted increase in aridity and temperature in southern Africa over the next century  ...  DdJ would like to thank Tuan Duong, Werner Smidt and Fourie Joubert for bioinformatics assistance, Michael Westbury for assistance with the PSMC analysis and Emily Humble for making their R scripts publicly  ... 
doi:10.1038/s41598-021-83823-8 pmid:33633171 pmcid:PMC7907399 fatcat:wgrehtfsgfh4nccjqludmkbgqy

Testing the caves-as-islands model in two cave-obligate invertebrates with a genomic approach [article]

Andras Balogh, Groves Bayne Dixon, Lam Ngo, Kirk S Zigler
2020 bioRxiv   pre-print
Our results support the idea of caves as natural laboratories for the study of parallel evolutionary processes.  ...  Organisms that have evolved to exist under these pressures typically exhibit a suite of convergent characteristics, including a loss or reduction of eyes and pigmentation.  ...  Data analysis was performed with the help of the Texas Advanced Computing Center. We thank Mikhail Matz for support as well as assistance with analysis and composition.  ... 
doi:10.1101/2020.04.08.032789 fatcat:zr6iz37dobfp3ni4vyarmmj3gi

Referee: Reference Assembly Quality Scores

2019 Genome Biology and Evolution  
Genome assemblies from next-generation sequencing technologies are now an integral part of biological research, but many sequencing and assembly processes are still error-prone.  ...  Although such errors are recognized when dealing with diploid genotype data, modern reference assemblies (which are represented as haploid sequences) lack any type of succinct quality assessment for every  ...  Referee adds a simple step between the assembly and analysis of a genome to improve the assembly for all purposes.  ... 
doi:10.1093/gbe/evz088 pmid:31028392 pmcid:PMC6535810 fatcat:ocyznoqnx5cr7oczxyxll6l64m

Hyena paleogenomes reveal a complex evolutionary history of cross-continental gene flow between spotted and cave hyena

Michael V. Westbury, Stefanie Hartmann, Axel Barlow, Michaela Preick, Bogdan Ridush, Doris Nagel, Thomas Rathgeber, Reinhard Ziegler, Gennady Baryshnikov, Guilian Sheng, Arne Ludwig, Ingrid Wiesel (+5 others)
2020 Science Advances  
Through the generation of population-level paleogenomes from late Pleistocene Eurasian cave hyena and genomes from modern African spotted hyena, we reveal the cross-continental evolutionary relationships  ...  Last, we find a number of introgressed loci that attained high frequencies within the recipient lineage, suggesting some level of adaptive advantage from admixture.  ...  We carried out PCA using single read identity by state (IBS) analyses in analysis of next generation sequencing data (ANGSD) v0.913 to avoid any biases differential coverage may cause in base calling  ... 
doi:10.1126/sciadv.aay0456 pmid:32201717 pmcid:PMC7069707 fatcat:gt3i3ctdunf75oefopyatjd5ay
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