GenomeQC

GenomeQC evaluates genome assemblies and gene structure annotations to quantify assembly completeness, contiguity, and annotation quality for genomic analyses.

Key Features:

• Integration of Multiple Metrics: Integrates various quantitative measures to evaluate genome assembly quality and gene annotation accuracy.
• Benchmarking Capabilities: Benchmarks assemblies and annotations against publicly available reference genomes to assess completeness and contiguity.
• Comprehensive Summaries with Graphics: Generates descriptive summaries accompanied by graphics for visualization and interpretation of quality metrics.
• Optimization for Genome Size: Optimized for small to medium-sized genomes (<2.5 Gb).
• Pre-computed Results: Includes pre-computed results for several maize genomes.
• Implementation: Implemented using R/Shiny 1.5.9 and Python 3.6.

Scientific Applications:

• Genomic Diversity Analysis: Supports comparative assessments of genome assemblies for studies of genetic diversity.
• Gene Expression and Annotation Studies: Assists evaluation of gene structure annotations used in gene expression characterization across individuals or tissues.
• Assembly Quality Control for Downstream Analyses: Provides metrics to validate assemblies and annotations prior to downstream biological interpretation and analyses.

Methodology:

Calculates a set of common assembly and annotation quality metrics to gauge completeness and contiguity and compares those metrics against reference genomes.