title: MToolBox: a highly automated pipeline for heteroplasmy annotation and prioritization analysis of human mitochondrial variants in high-throughput sequencing.
abstract: BACKGROUND
  The increasing availability of mitochondria-targeted and off-target sequencing data in whole-exome and whole-genome sequencing studies (WXS and WGS) has risen the demand of effective pipelines to accurately measure heteroplasmy and to easily recognize the most functionally important mitochondrial variants among a huge number of candidates. To this purpose, we developed MToolBox, a highly automated pipeline to reconstruct and analyze human mitochondrial DNA from high-throughput sequencing data.
  
  
  RESULTS
  MToolBox implements an effective computational strategy for mitochondrial genomes assembling and haplogroup assignment also including a prioritization analysis of detected variants. MToolBox provides a Variant Call Format file featuring, for the first time, allele-specific heteroplasmy and annotation files with prioritized variants. MToolBox was tested on simulated samples and applied on 1000 Genomes WXS datasets.
  
  
  METHODS
  MToolBox package is available at https://sourceforge.net/projects/mtoolbox/.
authors.affiliation: Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Department of Biosciences, University of Milan, 20133 Milan, Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, 70126 Bari, Department of Sciences and Technologies, University of Sannio, 82100 Benevento, Institute of Biomembranes and Bioenergetics, National Research Council, 70126 Bari, National Institute of Biostructures and Biosystems, 00136 Rome and Center of Excellence in Genomics for Biomedicine and Agri-food (CEGBA), University of Bari, 70126 Bari, Italy.
authors.forename: Claudia
authors.initials: C
authors.lastname: Calabrese
authors.affiliation: Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Department of Biosciences, University of Milan, 20133 Milan, Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, 70126 Bari, Department of Sciences and Technologies, University of Sannio, 82100 Benevento, Institute of Biomembranes and Bioenergetics, National Research Council, 70126 Bari, National Institute of Biostructures and Biosystems, 00136 Rome and Center of Excellence in Genomics for Biomedicine and Agri-food (CEGBA), University of Bari, 70126 Bari, Italy.
authors.forename: Domenico
authors.initials: D
authors.lastname: Simone
authors.affiliation: Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Department of Biosciences, University of Milan, 20133 Milan, Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, 70126 Bari, Department of Sciences and Technologies, University of Sannio, 82100 Benevento, Institute of Biomembranes and Bioenergetics, National Research Council, 70126 Bari, National Institute of Biostructures and Biosystems, 00136 Rome and Center of Excellence in Genomics for Biomedicine and Agri-food (CEGBA), University of Bari, 70126 Bari, Italy.
authors.forename: Maria Angela
authors.initials: MA
authors.lastname: Diroma
authors.affiliation: Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Department of Biosciences, University of Milan, 20133 Milan, Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, 70126 Bari, Department of Sciences and Technologies, University of Sannio, 82100 Benevento, Institute of Biomembranes and Bioenergetics, National Research Council, 70126 Bari, National Institute of Biostructures and Biosystems, 00136 Rome and Center of Excellence in Genomics for Biomedicine and Agri-food (CEGBA), University of Bari, 70126 Bari, Italy.
authors.forename: Mariangela
authors.initials: M
authors.lastname: Santorsola
authors.affiliation: Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Department of Biosciences, University of Milan, 20133 Milan, Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, 70126 Bari, Department of Sciences and Technologies, University of Sannio, 82100 Benevento, Institute of Biomembranes and Bioenergetics, National Research Council, 70126 Bari, National Institute of Biostructures and Biosystems, 00136 Rome and Center of Excellence in Genomics for Biomedicine and Agri-food (CEGBA), University of Bari, 70126 Bari, Italy.
authors.forename: Cristiano
authors.initials: C
authors.lastname: Guttà
authors.affiliation: Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Department of Biosciences, University of Milan, 20133 Milan, Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, 70126 Bari, Department of Sciences and Technologies, University of Sannio, 82100 Benevento, Institute of Biomembranes and Bioenergetics, National Research Council, 70126 Bari, National Institute of Biostructures and Biosystems, 00136 Rome and Center of Excellence in Genomics for Biomedicine and Agri-food (CEGBA), University of Bari, 70126 Bari, Italy.
authors.forename: Giuseppe
authors.initials: G
authors.lastname: Gasparre
authors.affiliation: Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Department of Biosciences, University of Milan, 20133 Milan, Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, 70126 Bari, Department of Sciences and Technologies, University of Sannio, 82100 Benevento, Institute of Biomembranes and Bioenergetics, National Research Council, 70126 Bari, National Institute of Biostructures and Biosystems, 00136 Rome and Center of Excellence in Genomics for Biomedicine and Agri-food (CEGBA), University of Bari, 70126 Bari, Italy Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Department of Biosciences, University of Milan, 20133 Milan, Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, 70126 Bari, Department of Sciences and Technologies, University of Sannio, 82100 Benevento, Institute of Biomembranes and Bioenergetics, National Research Council, 70126 Bari, National Institute of Biostructures and Biosystems, 00136 Rome and Center of Excellence in Genomics for Biomedicine and Agri-food (CEGBA), University of Bari, 70126 Bari, Italy Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Department of Biosciences, University of Milan, 20133 Milan, Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, 70126 Bari, Department of Sciences and Technologies, University of Sannio, 82100 Benevento, Institute of Biomembranes and Bioenergetics, National Research Council, 70126 Bari, National Institute of Biostructures and Biosystems, 00136 Rome and Center of Excellence in Genomics for Biomedicine and Agri-food (CEGBA), University of Bari, 70126 Bari, Italy.
authors.forename: Ernesto
authors.initials: E
authors.lastname: Picardi
authors.affiliation: Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Department of Biosciences, University of Milan, 20133 Milan, Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, 70126 Bari, Department of Sciences and Technologies, University of Sannio, 82100 Benevento, Institute of Biomembranes and Bioenergetics, National Research Council, 70126 Bari, National Institute of Biostructures and Biosystems, 00136 Rome and Center of Excellence in Genomics for Biomedicine and Agri-food (CEGBA), University of Bari, 70126 Bari, Italy Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Department of Biosciences, University of Milan, 20133 Milan, Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, 70126 Bari, Department of Sciences and Technologies, University of Sannio, 82100 Benevento, Institute of Biomembranes and Bioenergetics, National Research Council, 70126 Bari, National Institute of Biostructures and Biosystems, 00136 Rome and Center of Excellence in Genomics for Biomedicine and Agri-food (CEGBA), University of Bari, 70126 Bari, Italy Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Department of Biosciences, University of Milan, 20133 Milan, Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, 70126 Bari, Department of Sciences and Technologies, University of Sannio, 82100 Benevento, Institute of Biomembranes and Bioenergetics, National Research Council, 70126 Bari, National Institute of Biostructures and Biosystems, 00136 Rome and Center of Excellence in Genomics for Biomedicine and Agri-food (CEGBA), University of Bari, 70126 Bari, Italy.
authors.forename: Graziano
authors.initials: G
authors.lastname: Pesole
authors.affiliation: Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Department of Biosciences, University of Milan, 20133 Milan, Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, 70126 Bari, Department of Sciences and Technologies, University of Sannio, 82100 Benevento, Institute of Biomembranes and Bioenergetics, National Research Council, 70126 Bari, National Institute of Biostructures and Biosystems, 00136 Rome and Center of Excellence in Genomics for Biomedicine and Agri-food (CEGBA), University of Bari, 70126 Bari, Italy.
authors.forename: Marcella
authors.initials: M
authors.lastname: Attimonelli
mesh_terms: D004272:DNA, Mitochondrial / Q000737:chemistry*; D014644:Genetic Variation; D054629:Genome, Mitochondrial; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D058977:Molecular Sequence Annotation; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
chemical_list: D004272:DNA, Mitochondrial