PACVr

PACVr visualizes coverage depth and gene synteny of plastid (plastome) genome assemblies to assess assembly quality and confirm inverted repeat (IR) sequence equality.

Key Features:

• Coverage Depth Visualization: Visualizes coverage depth across a plastid genome assembly relative to the circular, quadripartite plastome structure and annotated genes to identify regions of reduced assembly confidence.
• Inverted Repeat Region Analysis: Confirms sequence equality between the two IR regions and visualizes gene synteny across IR boundaries to detect assembly discrepancies.
• Variable Window Approach: Implements a variable window approach to compute and display coverage depth at different calculation scales.
• Threshold-Based Identification: Supports specification of coverage thresholds to flag regions with coverage above or below defined values.

Scientific Applications:

• Assembly validation: Identification and localization of low-coverage or inconsistent regions to optimize plastid genome assemblies.
• Plastome sequence curation: Detection of assembly errors and confirmation of IR equality to improve the reliability of publicly available plastome sequences.
• Downstream genomic and evolutionary analyses: Verification of IR structure and gene synteny to ensure accuracy of data used in evolutionary and comparative studies.

Methodology:

Implemented as an R package that visualizes coverage depth and gene synteny on a circular, quadripartite plastome map using a variable window approach and user-specified coverage thresholds.