ngsTools protocols

View ngsTools computational protocol

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ngsTools specifications

Information


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

Subtools


  • HardMerge
  • SNVQ

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Versioning


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Documentation


Maintainer


  • person_outline Matteo Fumagalli <>

Publication for ngsTools

ngsTools in pipelines

 (6)
2018
PMCID: 5783331
PMID: 29364919
DOI: 10.1371/journal.pone.0190555

[…] 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 […]

2018
PMCID: 5844301
PMID: 29301862
DOI: 10.1534/g3.117.300334

[…] posterior probabilities calculated using the minind = 492, setmindepth = 492, and setmaxdepth = 4920 parameter set. genotype posterior probabilities were then used by the program ngsdist from the ngstools package to estimate all pairwise genetic distances. using the output file from the previous command, neighbor-joining trees were reconstructed with the genetic distances using the program […]

2018
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 […]

2017
PMCID: 5578843
PMID: 28860245
DOI: 10.1128/genomeA.00881-17

[…] libraries were sequenced on a miseq sequencer (illumina) using a miseq version 2.0 reagent kit (300 cycles). before assembly, paired-end reads (12,294,902) were filtered (see https://github.com/czh3/ngstools/blob/master/qualitycontrol.py) to obtain high-quality reads that were merged and adapter trimmed with seqprep (see https://github.com/jstjohn/seqprep). over 11.2 million merged or paired-end […]

2016
PMCID: 4911614
PMID: 27296726
DOI: 10.1038/ncomms11842

[…] help in the laboratory, as well as lex nederbragt and michael matschiner for their assistance with the abel cluster, matteo fumagalli and thorfinn korneliussen for their precious advice regarding ngstools and angsd, and alexei j. drummond for his insights on beast2 parametrization. we thank the ipev programme 109 (head: henri weimerskirch) for shared data collection on egg and chick mortality […]


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ngsTools in publications

 (24)
PMCID: 5783331
PMID: 29364919
DOI: 10.1371/journal.pone.0190555

[…] 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 […]

PMCID: 5844301
PMID: 29301862
DOI: 10.1534/g3.117.300334

[…] 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 […]

PMCID: 5726641
PMID: 29232403
DOI: 10.1371/journal.pone.0189417

[…] 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 […]

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

[…] using data from only a single randomly selected individual per burrow system in both pre- and post-eruption populations., next, we examined patterns of genetic diversity among populations using ngstools and custom python and r scripts. first, we calculated pairwise fst values for all populations of conspecifics. then, to assess differentiation among populations visually, we generated […]

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

[…] samples and samples with more than 50% missing genotypes were removed from the seeds data set., 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 [] […]


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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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