OrganPipe: An automated tool to facilitate the assembly, annotation, and curation of mitochondrial and chloroplast genomes

Analyzing organellar genomes (plastomes and mitogenomes) is important for understanding evolution, cellular function, and genetic diversity. Their stable mutation rates and inheritance patterns make them valuable for phylogenetic studies and taxonomic delimitation approaches. Assembling organellar genomes is considerably more straightforward than nuclear genomes due to their smaller size and simpler structure. To that end, existing tools like NOVOPlasty, GetOrganelle, and MitoHifi can handle different sequencing data types but have limitations, such as the reliance on single k-mers or reference genomes, which leads to suboptimal results and requires manual adjustments of parameters. OrganPipe, a newly developed pipeline, overcomes these challenges by allowing iterative assembly and annotation using multiple seeds and k-mers combinations. To demonstrate its capabilities, OrganPipe was used to assemble and annotate the first mitogenomes of two invertebrate species and the plastomes of two plant species, successfully circularizing and annotating the genomes with high accuracy, besides identifying key genomic features and correcting errors missed by other tools. Accessible to beginners and non-bioinformaticians, OrganPipe empowers diverse users to perform high-quality organelle genome analyses, supporting comprehensive exploration and efficient curation. This versatile tool advances large-scale genomic studies with its user-friendly and efficient design and is accessible at https://github.com/itvgenomics/OrganPipe. ^† joint first authors