Nuclear mitochondrial DNA insertion detection software tools | Whole-genome sequencing data analysis
The transfer of mitochondrial genetic material into the nuclear genomes of eukaryotes is a well-established phenomenon that has been previously limited to the study of static reference genomes. The recent advancement of high throughput sequencing has enabled an expanded exploration into the diversity of polymorphic nuclear mitochondrial insertions (NumtS) within human populations.
A method for identifying insertions of organellar origin from modern and ancient high-throughput sequencing data based on haplotype phasing. Odintifier represents the first integration of phasing algorithms into a reference-based organellar genome sequence assembly method, that furthermore allows for the simultaneous identification and reconstruction of organellar-derived inserted sequences.
This software is designed to identify and genotype nuclear insertions of mitochondrial origin from whole genome sequence data. It consists of two programs: dinumt (di-nu-mite), which identifies sites of insertions in a single sample and gnomit (geno-mite), which genotypes those sites across multiple samples. There is an additional program named clusterNumtsVcf which will merge sites identified in multiple samples into a single merged file for genotyping.