ArticleG3 (Bethesda, Md.)2026
WeavePop: a bioinformatics workflow to explore and analyze genomic variants of eukaryotic populations.
Article in G3 (Bethesda, Md.), 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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3 citing papers in PubMed.
- Meiosis-specific genes play roles in ploidy reduction inProceedings of the National Academy of Sciences of the United States of America · 2026Article
- Homeodomain protein Sxi1α independently controls cell-cell fusion and gene expression during sexual reproduction in Cryptococcus deneoformans.PLoS genetics · 2026Article
- Meiosis-specific genes play roles in ploidy reduction inbioRxiv : the preprint server for biology · 2025Article
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Abstract
Analyzing genomic variants in large datasets composed of short-read sequencing data is a process that requires multiple steps and computational tools, which makes it a complicated task that is difficult to reproduce across projects and laboratories. To address this need, we developed a reproducible and scalable Snakemake workflow called WeavePop, which aligns samples to selected references; obtains reference-based assemblies, annotations, and sequences; and identifies small variants and copy number variants in eukaryotic haploid organisms. All the results are integrated into a database that can be easily shared and explored through a graphical web interface provided alongside the workflow, making the discovery of variants in a population of study very simple. WeavePop is available from GitHub (https://github.com/magwenelab/WeavePop) for Linux operating systems. Here, we exemplify the use of WeavePop in a large collection of isolates of the pathogenic fungus Cryptococcus neoformans.
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