PopGenome pipeline

PopGenome specifications

Information


Unique identifier OMICS_08604
Name PopGenome
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data An almost de facto standard for whole-genome variation data is the variant call format (VCF), used, among others, by the 1000 genomes project and the UK10k project. PopGenome can read large SNP data sets stored in this format very efficiently, using indexes created with Tabix.
Input format FASTA, NEXUS, MEGA, MAF, and Phylip
Operating system Unix/Linux
Programming languages C, C++, R
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.1.6
Stability Stable
Requirements ff
Maintained Yes

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Documentation


Maintainer


  • person_outline Bastian Pfeifer <>

Publication for PopGenome

PopGenome IN pipelines

 (3)
2018
PMCID: 5859498
PMID: 29554870
DOI: 10.1186/s12864-018-4604-2

[…] and between u94-u100 genes (fig. 1). population genomics analyses including nucleotide diversity estimates, tajima’s d, achaz’s y, and hudson-kaplan recombination estimates were executed using the popgenome r package [28, 29, 60]. recombination detection analyses were performed using the dualbrothers package using a window length of 800 bp and a step size of 100 bp [61]., rna sequencing reads […]

2017
PMCID: 5389967
PMID: 28450881
DOI: 10.3389/fgene.2017.00044

[…] and fixed polymorphisms. we also computed the mean fst between populations for each category of markers. these statistics were calculated using vcftools (danecek et al., 2011) and the r package popgenome (pfeifer et al., 2014). an element was considered as complete if its size was at least 90% of the maximum size for its family. the vcflib script vcffilter6 was used to split vcfs […]

2017
PMCID: 5477509
PMID: 28537247
DOI: 10.1038/ncomms15323

[…] circos v0.62 (ref. 57). to minimize the bias for identification of genes under balancing selection, we further performed tajima's d calculation for all genes in the reference genome (msu v6.1) using popgenome v2.16 (ref. 58)., summary statistics for the portions of the gene (osasr3) sequenced by sanger method were performed by dnasp v5 (ref. 59). significance was tested with 10,000 coalescent […]

PopGenome institution(s)
Institute for Computer Science, Heinrich Heine University, Düsseldorf, Germany; Centre for Research in Agricultural Genomics, Bellaterra, Spain; Cluster of Excellence on Plant Sciences, Düsseldorf, Germany
PopGenome funding source(s)
This work was supported by the Spanish Ministerio de Ciencia e Innovación Grant CGL2009-09346 and by the German Research Foundation DFG grants EXC 1028 and CRC 680.

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