scalepopgen

scalepopgen performs automated population genomic analyses to infer population structure, migration events, and signatures of selection from biallelic SNP datasets.

Key Features:

• Automated Workflow Management: Orchestration via Nextflow with support for Conda, Singularity, and Docker for reproducible dependency management.
• Data Compatibility: Processes biallelic single nucleotide polymorphism (SNP) data in variant calling format (VCF) and PLINK binary files.
• Filtering: Automated procedures for filtering individuals and genotypes to produce high-quality input datasets.
• Population Structure Inference: Principal component analysis (PCA) and admixture analyses with identification of optimal K-values.
• TreeMix Analysis: Supports TreeMix with bootstrapping, migration edges, and determination of optimal numbers of migration events.
• Selection Signatures Identification: Implements single-population and pair-wise population comparison methods to detect genomic signatures of selection.
• Integration of Open-Source Tools: Integrates various open-source software and includes custom Python and R scripts for result collection and visualization.
• Execution Flexibility: Runnable on local machines and high-performance computing systems.

Scientific Applications:

• Population structure and admixture: Infers population clustering and admixture proportions to characterize population structure.
• Migration and gene flow: Identifies migration events and estimates migration edges to study gene flow among populations.
• Selection and evolutionary inference: Detects signatures of natural selection and supports analyses of demographic history and evolutionary processes.

Methodology:

Nextflow orchestrates execution of automated steps including filtering of individuals/genotypes, PCA, admixture (optimal K estimation), TreeMix analysis with bootstrapping and migration edge estimation, and selection scans, using containerization (Conda, Singularity, Docker) alongside integrated open-source tools and custom Python and R scripts.