NOVOWrap: an automated solution for plastid genome assembly and structure standardization

Plastid genomes play an important role in genomics and evolutionary biology. Next-generation sequencing has revolutionized plastid genomic data acquisition to the point that genome assembly has become a bottlenecks for widespread utilization of plastid genome data. To solve this problem, we developed an open-source, cross-platform tool known as, NOVOWrap, which includes both command-line and graphical interfaces for automatically assembling plastid genomes on personal computers. With minimal inputs, settings, and user intervention, NOVOWrap can automatically assemble plastid genomes, validate results and standardize the structure using affordable computer resources. The performance of this software has been successfully benchmarked against the plastid genomes of 11 species belonging to lycopods, gymnosperms, and angiosperms. This program is expected to liberate researchers from laborious and cumbersome computer manipulations and create reliable and standardized genomic data.

Methods
1. Use BarcodeFinder to evalute plastid genomes in NCBI RefSeq database;

2. Use NOVOWrap to assembly and generate synteny analyses results;

3. Use OGDRAW to visualize annotated plastid genomes;

4. Use GraphViz to draw unidirectional graph.