ArticleMolecular biology and evolution2024
A Fast, Reproducible, High-throughput Variant Calling Workflow for Population Genomics.
Article in Molecular biology and evolution, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed.
- A Mid-Atlantic Brook Trout (Salvelinus fontinalis) genome to advance conservation and comparative genomics.G3 (Bethesda, Md.) · 2026Article
- Variant calling in nonmodel organisms with snpArcher.Molecular biology and evolution · 2026Article
- Adaptation to seasonal drought in Arabis alpina is linked to the demographic history and climatic changes since the last glacial maximum.Molecular biology and evolution · 2026Article
- MKado: a toolkit for McDonald-Kreitman tests of natural selection.G3 (Bethesda, Md.) · 2026Article
- Rapid GC content evolution in rice through GC-biased gene conversion and selection for translation efficiency.Nature communications · 2026Article
- Stepwise emergence of recombination suppression precedes fissiparous asexuality in the planarian Schmidtea mediterranea.Nature communications · 2026Article
- A Recipe for a Good π. How to Properly Estimate Population Genetics Summary Statistics and Why we Should Systematically Report Them.Genome biology and evolution · 2026Article
- Ancient DNA from shells reveals delayed genomic erosion and rapid immune adaptation in the critically endangered black abalone.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Whole Genome Analyses of the Endangered Northern Abalone (Evolutionary applications · 2026Article
- Diversity and divergence of two sympatric, sibling octopus species.bioRxiv : the preprint server for biology · 2026Article
- SwarmGenomics: A Unified Pipeline for Individual-Based Whole-Genome Analyses.Molecular ecology resources · 2026Article
- Introgression and parental conflict shape repeated occurrences of postzygotic isolation in Mimulus.Current biology : CB · 2026Article
- Introgression across ploidies contributes to genetic diversity in introduced urbanbioRxiv : the preprint server for biology · 2026Article
- Parallel clines of chromosomal inversion frequencies in seaweed flies are associated with thermal variation.Heredity · 2026Article
- Germline de novo mutation rate of the highly heterozygous amphioxus genome.Molecular biology and evolution · 2026Article
- Estimating the Reduction in Genetic Diversity from Background Selection under Non-equilibrium Demography and Partial Selfing.Molecular biology and evolution · 2026Article
- Species delimitation within the Achnanthidium minutissimum complex (Bacillariophyta), based on morphological, molecular, and ecophysiological approaches.Journal of phycology · 2026Article
- Diversity at the HYP1 locus in potato cyst nematodes does not result from developmentally-programmed somatic mutations.PloS one · 2026Article
- Comparative population genomics reveals convergent adaptation across independent origins of avian obligate brood parasitism.Nature ecology & evolution · 2026Article
- Limited genomic signatures of population collapse in the critically endangered black abalone (Haliotis cracherodii).Molecular ecology · 2025Article
Corrections and comments
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The increasing availability of genomic resequencing data sets and high-quality reference genomes across the tree of life present exciting opportunities for comparative population genomic studies. However, substantial challenges prevent the simple reuse of data across different studies and species, arising from variability in variant calling pipelines, data quality, and the need for computationally intensive reanalysis. Here, we present snpArcher, a flexible and highly efficient workflow designed for the analysis of genomic resequencing data in nonmodel organisms. snpArcher provides a standardized variant calling pipeline and includes modules for variant quality control, data visualization, variant filtering, and other downstream analyses. Implemented in Snakemake, snpArcher is user-friendly, reproducible, and designed to be compatible with high-performance computing clusters and cloud environments. To demonstrate the flexibility of this pipeline, we applied snpArcher to 26 public resequencing data sets from nonmammalian vertebrates. These variant data sets are hosted publicly to enable future comparative population genomic analyses. With its extensibility and the availability of public data sets, snpArcher will contribute to a broader understanding of genetic variation across species by facilitating the rapid use and reuse of large genomic data sets.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.