Pipeliner

Pipeliner simulates next-generation sequencing (NGS) experiments to evaluate and compare SNP-calling and bioinformatics pipeline performance under varied experimental conditions.

Key Features:

• Simulation-based performance assessment: Simulates NGS experiments to assess pipeline performance and predict behavior under specified experimental conditions.
• Integration of tools: Incorporates publicly available software and custom-developed tools into configurable pipeline configurations.
• SNP-calling performance metrics: Computes recovery rates, sensitivity, and false discovery rates for both heterozygous and homozygous single nucleotide polymorphisms (SNPs).
• Scenario testing for experimental design: Enables exploration of scenarios such as doubling sequencing coverage while halving sample size and comparing false discovery rates across different SNP calling algorithms.
• Configurable pipelines: Supports customization of pipeline components and parameters to accommodate specific study requirements, species-specific considerations, and research objectives.

Scientific Applications:

• Sampling design and planning: Assesses the impact of sequencing coverage and sample size on SNP reliability to inform sampling and experimental design.
• Bioinformatics method evaluation: Compares alternative SNP calling algorithms and pipeline configurations to evaluate suitability for specific study systems and improve NGS data interpretation accuracy.

Methodology:

Implemented in C++, Pipeliner integrates existing bioinformatics tools and custom software and performs simulations grounded in realistic modeling of sequencing experiments.