An effective workflow with customizable parameters and able to analyze multiple samples in a single run. MToolBox is the only tool that generates as output a VCF file, the standard format for large-scale genotyping information, suitably customized for mitochondrial data, by including the heteroplasmy fraction and its related confidence interval. Additionally, MToolBox provides the user with essential analyses of reconstructed mitochondrial genomes, i.e. haplogroup assignment and variant prioritization, exploiting a broad collection of annotation resources. Thus, MToolBox may provide a valuable support for the recognition of candidate mitochondrial mutations in clinical studies.
Conducts analysis for human mitochondrial DNA (mtDNA) next generation sequencing (NGS) data. mtDNA-Server is useful for the discovery of heteroplasmic sites, contamination determination and numerous quality control (QC) statistics. It can serve for the evaluation of data from whole genome sequencing investigations for potential contamination and is therefore not limited to target mtDNA sequencing.
A simple web-based tool for analyzing heteroplasmy using sequences generated by second generation sequencing technology, specifically designed for studying the functional potential of mtDNA heteroplasmy in humans. MitoBamAnnotator receives files describing the alignment of mtDNA next generation sequences to the mtDNA genome or a list of mutated positions as input, and provides a richly annotated report of suspected heteroplasmic sites. Users control the filtration process by modifying the filtration parameters, and receive the results in a compact table which can be further filtered using spreadsheet editing programs such as Microsoft Excel or open-access equivalents.
Proposes a platform for forensic mitochondrial DNA (mtDNA) analysis that uses a massively parallel sequencing (MPS) method. GeneMarker HTS allows (i) the browsing through the investigated data, (ii) the alignment of the homopolymeric sequences, single nucleotide polymorphisms (SNPs) and INDELs, (iii) the identification of phylogenetically correct primary haplotypes or heteroplasmic variants, (iv) the generation of reports and (v) the exploitation of the results for database searching.
A tool designed to provide clinically relevant information distributed in disparate resources for understanding and annotating human mitochondrial DNA variations. The pipeline has two components: a command-line component that provides automation for alignment of NGS reads to the modified rCRS; and an online version that provides a comprehensive genetic report of mitochondrial variants, which includes information about the corresponding mutation, gene, associated phenotype and population frequency. mit-o-matic also reports the estimated haplogroup, disease associated variations and heteroplasmic sites.
An open-source software tool that can reliably and easily extract mitochondrial genome information from exome and whole genome sequencing data. MitoSeek evaluates mitochondrial genome alignment quality, estimates relative mitochondrial copy numbers and detects heteroplasmy, somatic mutation and structural variants of the mitochondrial genome. MitoSeek can be set up to run in parallel or serial on large exome sequencing datasets.
Estimates Mitochondrial DNA (mtDNA) copy number highly accurately using 0.1% of the genome. fastMitoCalc is an application that takes advantage of the indexing of sequencing alignment files, focusing on a small subset of the nuclear genome to estimate autosomal DNA coverage accurately. It analyzes hundreds of thousands of genomes currently being sequenced by large research consortia, and facilitates association studies of mtDNA copy number with quantitative trait values or nuclear variants.