# WeavePop: a bioinformatics workflow to explore and analyze genomic variants of eukaryotic populations

## TL;DR

WeavePop is a bioinformatics workflow that simplifies the analysis of genomic variants in eukaryotic populations using short-read sequencing data.

## Contribution

The novel contribution is a reproducible and scalable Snakemake workflow for variant discovery in haploid eukaryotes.

## Key findings

- WeavePop integrates genomic data into a database accessible via a web interface for easy exploration.
- The workflow was successfully applied to a large collection of Cryptococcus neoformans isolates.
- It identifies small and copy number variants while supporting reference-based assemblies and annotations.

## 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.

Graphical AbstractFor image description, please refer to the figure legend and surrounding text.