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ngsTools specifications


Unique identifier OMICS_02248
Name ngsTools
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input format BAM,SAM
Operating system Unix/Linux
Programming languages C, C++
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes


  • HardMerge
  • SNVQ




No version available



  • person_outline Matteo Fumagalli

Publication for ngsTools

ngsTools citations


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

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

[…] 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 likelihood analyses with RAxML v8.2.10 (), specifying th […]


Genome wide analyses of the Bemisia tabaci species complex reveal contrasting patterns of admixture and complex demographic histories

PLoS One
PMCID: 5783331
PMID: 29364919
DOI: 10.1371/journal.pone.0190555

[…] uality data and calculate genotype posterior probabilities with an informative prior under the assumption of Hardy Weinberg Equilibrium (HWE). We estimated the covariance matrix between samples using ngsTools [], which takes data uncertainty into account. From such matrix, principal components were calculated and plotted using custom R scripts. This demonstrates that our main findings are not bias […]


Multiple Origin but Single Domestication Led to Oryza sativa

PMCID: 5844301
PMID: 29301862
DOI: 10.1534/g3.117.300334
call_split See protocol

[…] lign around INDEL regions ().Using the processed alignment files, genotype probabilities were calculated with the program ANGSD ver. 0.913 (). The genotype probabilities were then used by the program ngsTools () to conduct population genetic analysis. To estimate θ, ngsTools uses the site frequency spectrum as a prior to calculate allele frequency probabilities. Usually site frequency spectrum req […]


Genomics clarifies taxonomic boundaries in a difficult species complex

PLoS One
PMCID: 5726641
PMID: 29232403
DOI: 10.1371/journal.pone.0189417
call_split See protocol

[…] supplementary section (). PC analyses were conducted on subsampled BAM files using genotype posterior probabilities calculated with a uniform prior (doPost 2). The ngscovar [] function implemented in ngstools [] was used to calculate a covariance matrix from called genotypes. The matrix was then plotted in R [].Admixture analyses were conducted on samples (based on each hierarchical subsampling) u […]


Genomic data reveal a loss of diversity in two species of tuco tucos (genus Ctenomys) following a volcanic eruption

Sci Rep
PMCID: 5701162
PMID: 29176629
DOI: 10.1038/s41598-017-16430-1

[…] plotted distributions of Tajima’s D for each population sampled. This statistic, which can reflect both past demographic events and selection, was estimated across 100-bp sliding window regions using ngsTools; use of a distribution of values for Tajima’s D allows for more robust assessments of demographic history than a single mean estimate of this parameter,. We also generated pairwise mismatch d […]


The interplay of demography and selection during maize domestication and expansion

Genome Biol
PMCID: 5683586
PMID: 29132403
DOI: 10.1186/s13059-017-1346-4

[…] We first evaluated population structure using principal component analysis (PCA) with ngsCovar [] in ngsTools [] based on the matrix of posterior probabilities of SNP genotypes produced in Analysis of Next Generation Sequencing Data (ANGSD) v.0.614 [], and then utilized NGSadmix v.32 [] to investigat […]


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ngsTools institution(s)
Department of Integrative Biology, University of California, Berkeley, CA, USA; Department of Statistics, University of California, Berkeley, CA, USA; Department of Biology, University of Copenhagen, Copenhagen, Denmark
ngsTools funding source(s)
Supported by a NIH (3R01HG03229-07) grant, an EMBO Long-term Fellowship ALTF 2011-229 and an NIH Genomics Training Grant (T32HG000047-13).

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