PEMer

PEMer detects structural variants in genomic sequences from paired-end sequencing reads to map and characterize genomic structural variation.

Key Features:

• PEMer workflow: Implements a sensitive workflow for detecting structural variants from paired-end sequence reads using a coverage-adjusted multi-cutoff scoring strategy.
• Simulation-based error models: Uses simulation-based error models to assign confidence values to each detected structural variant.
• Platform compatibility: Supports multiple next-generation sequencing platforms.
• Relative insensitivity to base-calling errors: Shows relative insensitivity to base-calling errors as assessed by simulation studies.
• Back-end database: Provides a back-end database for storage and retrieval of genomic data and structural-variant results.

Scientific Applications:

• Structural variant discovery: Detection and reconstruction of structural variants from paired-end sequencing data.
• Population genomics: Mapping genomic structural variation in population-scale projects such as the 1000 Genomes Project.
• Disease and phenotype studies: Identifying genetic variations that may contribute to disease susceptibility or phenotypic differences.
• Evolutionary biology: Characterizing structural variation to study genetic diversity and evolutionary processes.

Methodology:

Processes paired-end sequence reads, applies a coverage-adjusted multi-cutoff scoring strategy for structural-variant reconstruction, employs simulation-based error models to assign confidence values and evaluate base-calling error effects, and stores results in a back-end database.