PAPipe

PAPIpe: Automated Population Genetic Analysis Pipeline

PAPIpe automates population genetic analysis by integrating read trimming and mapping, genetic variant calling, data filtering, and format conversion into a unified workflow.

Key Features:

• Automated Processing Pipeline: Integrates read trimming, read mapping, genetic variant calling, data filtering, and format conversion in a single workflow.
• Population Genetic Analyses: Supports Principal Component Analysis (PCA), Phylogenetic Analysis, Population Tree Analysis, Population Structure Analysis, Linkage Disequilibrium Decay Analysis, Selective Sweep Analysis, Population Admixture Analysis, Sequentially Markovian Coalescent Analysis, and Fixation Index Analysis.

Scientific Applications:

• Population Structure and Evolution: Analyzes evolutionary relationships, genetic diversity, adaptation, selection pressures, gene flow, and admixture among populations.

Methodology:

PAPIpe serializes sequential analytical steps into an automated workflow, executing preprocessing, variant detection, and downstream population genetic analyses to generate integrated results from high-throughput sequencing data.