Abstract

Plastid genomes are unique to plants and play an important role in genomics and evolutionary biology. Next-generation sequencing has revolutionized plastid genome data acquisition in a way that genome assembly and annotation became bottlenecks for large plastid genome data usage. Here we develop a novel open-source, cross-platform tool, NOVOWrap, with both command-line and graphical user interfaces for plastid genome automatic assembly using personal computers. With minimum inputs and user intervention, NOVOWrap could automatically assemble plastid genomes, validate results and standardize the structure with affordable computer resources. The performance of the software has been successfully benchmarked against eleven plastid genomes of species belonging to lycopods, gymnosperms, and angiosperms. The program is expected to liberate researchers from laborious computer manipulations and create reliable and standard genomic data.