OrganPipe

OrganPipe automates the assembly, annotation, and curation of mitochondrial and chloroplast genomes through iterative assembly with multiple seeds and k-mer combinations.

Key Features:

• Iterative Assembly: The pipeline performs iterative assembly using multiple seeds and k-mer combinations to overcome limitations of tools relying on single k-mers or reference genomes.
• Genome Circularization: OrganPipe successfully circularizes organellar genomes during assembly.
• Automated Annotation: The pipeline annotates assembled genomes with high accuracy.
• Error Correction: OrganPipe identifies and corrects errors missed by other tools, including key genomic features.

Scientific Applications:

• Mitogenome Assembly: OrganPipe assembled and annotated the first mitogenomes of two invertebrate species.
• Plastome Assembly: The pipeline assembled and annotated the plastomes of two plant species.
• Phylogenetic Studies: The tool supports phylogenetic studies and taxonomic delimitation approaches through accurate organellar genome analysis.
• Large-Scale Genomic Studies: OrganPipe advances large-scale genomic studies with efficient organelle genome curation.

Methodology:

OrganPipe uses iterative assembly and annotation with multiple seeds and k-mer combinations.