NOVOPlasty

NOVOPlasty assembles organelle genomes from whole genome sequencing data and detects heteroplasmy in mitochondrial and chloroplast genomes.

Key Features:

• Organelle genome assembly: Assembles short circular genomes from whole genome sequencing data using a seed-and-extend algorithm starting from a related or distant single seed sequence.
• Heteroplasmy detection: Detects intra-individual polymorphisms within mitochondrial and chloroplast genomes more accurately than previous methods.
• Haplotype reconstruction: Is the first tool able to completely or partially reconstruct the sequence for each mitochondrial haplotype by assembling the sequence around each detected polymorphic site and looking for linkage among polymorphic sites.
• Variance calling: Functions as a variance caller for short circular genomes.
• Circular contig output: Produces organelle genome assemblies as one circular high quality contig.

Scientific Applications:

• Phylogenetic studies: Produces organelle genome assemblies used in phylogenetic studies.
• Food identification: Supports food identification applications through organelle genome analysis.
• Disease research: Enables study of mitochondrial genome polymorphisms linked to multiple severe disorders through heteroplasmy detection.
• Evolutionary studies: Facilitates evolutionary studies through analysis of intra-individual polymorphisms and heteroplasmy patterns.
• Forensic science: Supports forensic science applications through mitochondrial genome variation analysis.

Methodology:

NOVOPlasty uses a seed-and-extend algorithm that assembles organelle genomes from whole genome sequencing data, starting from a related or distant single seed sequence. For heteroplasmy detection, the method assembles the sequence around each detected polymorphic site and looks for linkage among polymorphic sites to reconstruct haplotypes.