Abstract
Plastid genomes typically display a circular, quadripartite structure with two inverted repeat regions, which challenges automatic assembly procedures. The correct assembly of plastid genomes is a prerequisite for the validity of subsequent analyses on genome structure and evolution. The average coverage depth of a genome assembly is often used as an indicator of assembly quality. Visualizing coverage depth across a draft genome is a critical step, which allows users to inspect the quality of the assembly and, where applicable, identify regions of reduced assembly confidence. Despite the interplay between genome structure and assembly quality, no contemporary, user-friendly software tool can visualize the coverage depth of a plastid genome assembly while taking its quadripartite genome structure into account. A software tool is needed that fills this void.
Document Type
Article
Source Publication
BMC Bioinformatics
Version
Published Version
Publication Date
1-1-2020
Volume
21
Issue
1
Creative Commons License
This work is licensed under a Creative Commons Attribution-NonCommercial-No Derivative Works 4.0 International License.
Rights
Notice: This material may be protected by copyright law (Title 17 U.S. Code).
Recommended Citation
Gruenstaeudl, M., & Jenke, N. (2020). PACVr: Plastome assembly coverage visualization in R. BMC Bioinformatics, 21(1), 207. https://doi.org/10.1186/s12859-020-3475-0
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