SwarmGenomics

SwarmGenomics integrates seven modules for reference-based genome assembly and individual-based genetic analyses including heterozygosity estimation, runs of homozygosity detection, Pairwise Sequentially Markovian Coalescent (PSMC) analysis, unmapped reads classification, repeat analysis, mitochondrial genome assembly, and nuclear mitochondrial DNA segment (NUMT) identification.

Key Features:

• Heterozygosity Estimation: Estimates genome-wide heterozygosity from whole-genome sequencing data.
• Runs of Homozygosity Detection: Detects runs of homozygosity to infer inbreeding history.
• PSMC Analysis: Performs Pairwise Sequentially Markovian Coalescent analysis to reconstruct historical population size changes.
• Unmapped Reads Classification: Classifies reads that do not map to the reference genome.
• Repeat Analysis: Analyzes repetitive elements including transposable element activity.
• Mitochondrial Genome Assembly: Assembles mitochondrial genomes from whole-genome sequencing data.
• NUMT Identification: Identifies nuclear mitochondrial DNA segments.

Scientific Applications:

• Population Genetics: Enables estimation of genetic diversity and historical demography in diploid, non-model species.
• Evolutionary Biology: Supports inference of historical population size changes and transposable element dynamics.
• Conservation Genomics: Facilitates assessment of inbreeding history and genetic diversity for conservation purposes.
• Microbial Contamination Detection: Identifies potential microbial contamination through unmapped reads classification.

Methodology:

The pipeline follows a reference-based assembly approach with modular architecture allowing independent or complete workflow execution. Methods for each module are implemented through integration of specialized bioinformatics tools; specific algorithmic details for individual modules are not explicitly stated in the sources.