The mitochondrion, also referred to as the powerhouse, is the main cellular machinery for ATP production. However, several studies have demonstrated that this organelle plays important roles in cellular metabolism and homeostasis, such as the synthesis of metabolic precursors, calcium regulation, reactive oxygen species production, immune signaling, and apoptosis. The human mitochondrial DNA molecule (mtDNA) is a circular double-stranded desoxyribonucleic acid of approximately 16kb, which appears to constitute a low complexity genome due to its short length and few repetitive regions, and a very efficient extra-chromosomal molecule because of its high proportion of protein-encoding genes. The mtDNA is also considered a polyploid genome, as each cell can bears multiple mitochondria with diverse polymorphic DNA molecules, which is commonly known as heteroplasmy. The mitochondrial genetic information has also been associated with diseases and aging in humans, and its heteroplasmy manifests critical protein expression points. Moreover, several mtDNA mutations have been associated with development of pathological conditions such as the congestive heart failure. Similarly, evidence of C150T mutation favoring longevity has been widely discussed, therefore heteroplasmy detection has represented the main approach in mitochondrial studies in health and longevity. Heteroplasmy detection presents a challenge for long-reads sequencing technologies, such as Oxford-Nanopore (ONT), due to the production of prone-error reads, consequently Sanger and Next Generation Sequencing (NGS) has dominated mitochondrial research the last years, nonetheless ONT recently presented a new pore chemistry R10 which coupled with HERRO correction can achieve read qualities of Q30 and researchers have highlighted the improvement in epigenetic modifications, Single Nucleotide Polymorphism (SNP) and Structural Variations (SV) detection. As a consequence, most open source tools for mtDNA processing have been developed for short reads technologies, E.g NOVOplasty, MITObim, MEANGS, Norgal and MitoZ. MitoHiFi, published in 2022, represented the first pipeline proposal for assembly and annotation of mitogenome for long reads, but it works with PacBio HiFi reads. Thus, in this study, we introduce MITNANEX a novel pipeline designed for the extraction of mitochondrial ONT reads and the detection of point mutations and ancestry composition. Here, we used MITNANEX for the genetic assembling and analysis of mitogenomes of Centenarians, human older than 100-years of age, aiming to identify variants associated with longevity, as well as, their genetic lineages. We successfully assembled and annotated a circular mtDNA molecule of 16,568 bp, belonging to a 105-YO female-human, with a 178x coverage and found mutations correlated with longevity, as well as mapped haplotypes.