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WeavePop is a Snakemake workflow that maps short sequencing reads of multiple haploid eukaryotic genomes to selected reference genomes and analyzes the genomic variants between them. The core analysis is done by Snippy to obtain alignment files (BAM), variant calling files (VCFs), and reference-based assemblies. From these results, WeavePop analyzes the mapping quality and depth, annotates the assemblies with Litoff using the corresponding reference genome annotation, extracts the DNA and amino acid sequences of all transcripts using AGAT, annotates the effects of the small variants with SnpEff, calls Copy-Number Variants, generates a variety of useful diagnostic plots, and integrates all the results into an DuckDB (SQL) database. The database allows users to easily explore the results using WeavePop-Shiny, an interactive web app, or the command-line interface WeavePop-CLI.
- Home
- Basic usage
- Working with multiple projects and runs
- Execution profiles
- SLURM execution
- Installation
- Input files
- Configuration
- Output
- Testing
- WeavePop-Shiny
- WeavePop-CLI
- Workflow steps
Comment on any issue, contribution, or question on the Issues page
WeavePop: A bioinformatics workflow to explore and analyze genomic variants of eukaryotic populations Claudia Zirión-Martínez, Paul M. Magwene bioRxiv 2025.08.15.670593; doi: https://doi.org/10.1101/2025.08.15.670593
WeavePop is licensed under the GNU license.