Seal

Seal simulates next-generation sequencing (NGS) reads and evaluates short-read alignment algorithms to compare mapping accuracy and computational performance across varied sequencing conditions.

Key Features:

• Simulation Capabilities: Simulates NGS runs while varying sequencing error rates, insertions and deletions (indels), and coverage levels.
• Comprehensive Evaluation Criteria: Compares alignment tools that produce differing output structures (single best alignment versus multiple alignments) using criteria that accommodate these differences.
• Performance Metrics: Quantifies alignment performance using accuracy and runtime efficiency metrics.
• Broad Application Scope: Applies simulations and evaluations to assess algorithms used in deep sequencing applications, including genomic variant identification.

Scientific Applications:

• Alignment software benchmarking: Enables comparison of aligners such as Bowtie, BWA, mr- and mrsFAST, Novoalign, SHRiMP, and SOAPv2 under defined sequencing scenarios.
• Assessment of variant-calling impact: Evaluates how sequencing error rates, indels, and coverage affect algorithm performance relevant to genomic variant identification.

Methodology:

Seal generates simulated NGS data with varied sequencing error rates, indels, and coverage, then evaluates alignment tools using predefined criteria that account for differing output structures, accuracy, and runtime efficiency.