ArticleBioinformatics (Oxford, England)2024
AncestryGrapher toolkit: Python command-line pipelines to visualize global- and local- ancestry inferences from the RFMIX version 2 software.
Article in Bioinformatics (Oxford, England), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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4 citing papers in PubMed.
- Haplotype-resolved genome assemblies of BJ and IMR-90 human fibroblast cell lines reveal extensive structural variation and enable reanalysis of historical sequencing data.Nucleic acids research · 2026Article
- Genome sequencing of 35,024 predominantly African ancestry persons addresses gaps in genomics and healthcare.medRxiv : the preprint server for health sciences · 2025Article
- Polaris: Polarization of ancestral and derived polymorphic alleles for inferences of extended haplotype homozygosity in human populations.Bioinformatics (Oxford, England) · 2025Article
- Diploid genome assembly of human fibroblast cell lines enables clone specific variant calling, improved read mapping and accurate phasing.bioRxiv : the preprint server for biology · 2025Article
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Abstract
summaryAdmixture is a fundamental process that has shaped levels and patterns of genetic variation in human populations. RFMIX version 2 (RFMIX2) utilizes a robust modeling approach to identify the genetic ancestries in admixed populations. However, this software does not have a built-in method to visually summarize the results of analyses. Here, we introduce the AncestryGrapher toolkit, which converts the numerical output of RFMIX2 into graphical representations of global and local ancestry (i.e. the per-individual ancestry components and the genetic ancestry along chromosomes, respectively).
resultsTo demonstrate the utility of our methods, we applied the AncestryGrapher toolkit to visualize the global and local ancestry of individuals in the North African Mozabite Berber population from the Human Genome Diversity Panel. Our results showed that the Mozabite Berbers derived their ancestry from the Middle East, Europe, and sub-Saharan Africa (global ancestry). We also found that the population origin of ancestry varied considerably along chromosomes (local ancestry). For example, we observed variance in local ancestry in the genomic region on Chromosome 2 containing the regulatory sequence in the MCM6 gene associated with lactase persistence, a human trait tied to the cultural development of adult milk consumption. Overall, the AncestryGrapher toolkit facilitates the exploration, interpretation, and reporting of ancestry patterns in human populations. AVAILABILITY AND IMPLEMENTATION: The AncestryGrapher toolkit is free and open source on https://github.com/alisi1989/RFmix2-Pipeline-to-plot.
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