WeavePop: a bioinformatics workflow to explore and analyze genomic variants of eukaryotic populations
Year: 2026
Type: article
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.
Source: G3 Genes Genomes Genetics
Authors: Claudia Zirión-Martínez, Paul M Magwene
Institution: Duke University
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $2,709
OpenAlex ID: W7128770524