ANGSD statistics

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Citations per year

Number of citations per year for the bioinformatics software tool ANGSD
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Tool usage distribution map

This map represents all the scientific publications referring to ANGSD per scientific context
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Associated diseases

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Protocols

ANGSD specifications

Information


Unique identifier OMICS_16021
Name ANGSD
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format BAM, VCF, CRAM
Output format TXT
Operating system Unix/Linux, Mac OS, Windows
Programming languages C, C++
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Requirements
ZLIB
Maintained Yes

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Versioning


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Documentation


Maintainer


  • person_outline Thorfinn Sand Korneliussen

Publications for ANGSD

ANGSD citations

 (79)
library_books

Comparative Population Genomics Analysis of the Mammalian Fungal Pathogen Pneumocystis

2018
MBio
PMCID: 5941068
PMID: 29739910
DOI: 10.1128/mBio.00381-18

[…] relationships between isolates using principal-component analysis (PCA) implemented in SNPRelate v.1.10.2 (). Summary statistics were computed using VCFtools (). Neutrality tests were performed using ANGSD (). Genetic clustering was performed using NGSAdmix () and fastStructure ().The linkage disequilibrium was calculated as r2, which indicates the square of the correlation coefficient between two […]

call_split

Ancient DNA from Giant Panda (Ailuropoda melanoleuca) of South Western China Reveals Genetic Diversity Loss during the Holocene

2018
Genes
PMCID: 5924540
PMID: 29642393
DOI: 10.3390/genes9040198
call_split See protocol

[…] gnment (“sort”) and collapse sequences with identical 5’ mapping coordinates (“rmdup”). Finally, a consensus sequence was generated for each individual, based on maximum effective read depth [] using ANGSD v0.916 []. Besides assembling the NGS short reads, we retrieved three assembled giant panda mitochondrial genomes from GenBank [,,] which, together with the sequences from our two individuals, p […]

library_books

Real time DNA barcoding in a rainforest using nanopore sequencing: opportunities for rapid biodiversity assessments and local capacity building

2018
GigaScience
PMCID: 5905381
PMID: 29617771
DOI: 10.1093/gigascience/giy033

[…] mbly. For the reference-based mapping, we used BWA 0.7.15 (BWA, RRID:SCR_010910) [, ] to align the reads to the reference, samtools 1.3 (SAMTOOLS, RRID:SCR_002105) [] to process the mapping file, and ANGSD [] to call the consensus sequence. The de novo assembly of each amplicon was carried out using Canu (Canu, RRID:SCR_015880) [, ], with parameters fitting for our application. Given that we used […]

call_split

Oat evolution revealed in the maternal lineages of 25 Avena species

2018
Sci Rep
PMCID: 5844911
PMID: 29523798
DOI: 10.1038/s41598-018-22478-4
call_split See protocol

[…] wheat organelle genome sequences using Bowtie2 to generate a SAM file. Based on the SAM file, SAMtools was used to create, sort and index BAM files for SNP calling. SNP calls were conducted using the ANGSD pipeline with the parameter settings given in Electronic Supplementary Material (ESM), and they were based on allele frequencies that were estimated with genotype likelihoods from the sorted.bam […]

library_books

Extended and Continuous Decline in Effective Population Size Results in Low Genomic Diversity in the World’s Rarest Hyena Species, the Brown Hyena

2018
Mol Biol Evol
PMCID: 5913678
PMID: 29528428
DOI: 10.1093/molbev/msy037

[…] icted to single nucleotide polymorphisms (SNPs) occurring in at least two individuals. This was done to remove singletons, which could represent sequencing errors. We computed genotype likelihoods in ANGSD and converted outputs to a covariance matrix using ngsTools (). Covariance matrices were converted into PCA outputs and visualized using R (). For the phylogenetic analyses, we performed Maximum […]

library_books

Strong phenotypic plasticity limits potential for evolutionary responses to climate change

2018
Nat Commun
PMCID: 5843647
PMID: 29520061
DOI: 10.1038/s41467-018-03384-9

[…] In order to assess footprints of selection in different gene repertoires, we quantified nucleotide diversity (π) and Tajima’s D for each transcript expressed in the abdomen. We used angsd to calculate pairwise nucleotide diversity π and Tajima’s D from the abdomen RNA-seq reads (aligned using Bowtie2 v. 2.2.3 to our Evigene-enriched reference transcriptome), restricting analyses […]


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ANGSD institution(s)
Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark; Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark; Department of Integrative Biology and Statistics, UC-Berkeley, Berkeley, CA, USA
ANGSD funding source(s)
Supported by Danish National Research Foundation (DNRF94), the Villum Foundation, and grant 2R14003229-07 from the National Institutes of Health.

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