WeavePop

WeavePop analyzes genomic variants in eukaryotic populations through a reproducible and scalable Snakemake workflow.

Key Features:

• Read alignment: Aligns samples to selected references.
• Assembly generation: Obtains reference-based assemblies, annotations, and sequences.
• Variant identification: Identifies small variants and copy-number variants in eukaryotic haploid organisms.
• Database integration: Integrates all results into a database.

Scientific Applications:

• Population genomics: Enables discovery of variants in a population of study.
• Pathogen analysis: Supports analysis of large collections of isolates of pathogenic fungi such as Cryptococcus neoformans.

Methodology:

WeavePop is implemented as a Snakemake workflow.