GetOrganelle

GetOrganelle assembles plastid and mitochondrial genomes de novo from whole genome sequencing data using baiting and iterative mapping to recruit organelle reads and reconstruct circular genome configurations.

Key Features:

• Baiting and iterative mapping: Uses a baiting and iterative mapping approach to recruit organelle-associated reads from whole genome sequencing (WGS) data.
• De novo assembly: Performs de novo assembly on the recruited organelle reads to reconstruct genome sequences.
• Assembly graph filtering and disentanglement: Filters and disentangles the assembly graph to isolate organelle genome paths and resolve alternative connections.
• Multiple circular configurations: Outputs all possible circular organelle genome configurations to represent alternative structural arrangements.
• Plastid and mitochondrial assembly: Assembles circular plastomes and complete mitochondrial genomes from WGS data.
• Performance evaluation: Reassembled circular plastomes in 47 of 50 published plant datasets and showed superior mapping assessments compared to NOVOPlasty.

Scientific Applications:

• Plastome reconstruction: Reconstruction of circular plastid genomes from WGS data for plant genomics.
• Mitochondrial genome assembly: Assembly of complete mitochondrial genomes from WGS datasets.
• Organelle structural analysis: Exploration and representation of alternative circular genome configurations and structural arrangements.
• Comparative genomics and evolution: Provision of organelle genome sequences for comparative genomics and organelle evolution studies.

Methodology:

Employs baiting and iterative mapping to recruit organelle reads from WGS data, performs de novo assembly of recruited reads, filters and disentangles the assembly graph, and outputs possible circular genome configurations; evaluation used mapping assessments and comparison with NOVOPlasty.