{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,26]],"date-time":"2026-06-26T20:35:29Z","timestamp":1782506129436,"version":"3.54.5"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"21","license":[{"start":{"date-parts":[[2016,11,7]],"date-time":"2016-11-07T00:00:00Z","timestamp":1478476800000},"content-version":"vor","delay-in-days":847,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: 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.<\/jats:p>\n               <jats:p>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.<\/jats:p>\n               <jats:p>Availability and implementation: MToolBox package is available at https:\/\/sourceforge.net\/projects\/mtoolbox\/ .<\/jats:p>\n               <jats:p>Contact: \u00a0marcella.attimonelli@uniba.it<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu483","type":"journal-article","created":{"date-parts":[[2014,7,16]],"date-time":"2014-07-16T00:23:13Z","timestamp":1405470193000},"page":"3115-3117","source":"Crossref","is-referenced-by-count":193,"title":["MToolBox: a highly automated pipeline for heteroplasmy annotation and prioritization analysis of human mitochondrial variants in high-throughput sequencing"],"prefix":"10.1093","volume":"30","author":[{"given":"Claudia","family":"Calabrese","sequence":"first","affiliation":[{"name":"1 Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, 2 Department of Biosciences, University of Milan, 20133 Milan, 3 Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, 70126 Bari, 4 Department of Sciences and Technologies, University of Sannio, 82100 Benevento, 5 Institute of Biomembranes and Bioenergetics, National Research Council, 70126 Bari, 6 National Institute of Biostructures and Biosystems, 00136 Rome and 7 Center of Excellence in Genomics for Biomedicine and Agri-food (CEGBA), University of Bari, 70126 Bari, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Domenico","family":"Simone","sequence":"additional","affiliation":[{"name":"1 Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, 2 Department of Biosciences, University of Milan, 20133 Milan, 3 Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, 70126 Bari, 4 Department of Sciences and Technologies, University of Sannio, 82100 Benevento, 5 Institute of Biomembranes and Bioenergetics, National Research Council, 70126 Bari, 6 National Institute of Biostructures and Biosystems, 00136 Rome and 7 Center of Excellence in Genomics for Biomedicine and Agri-food (CEGBA), University of Bari, 70126 Bari, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria Angela","family":"Diroma","sequence":"additional","affiliation":[{"name":"1 Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, 2 Department of Biosciences, University of Milan, 20133 Milan, 3 Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, 70126 Bari, 4 Department of Sciences and Technologies, University of Sannio, 82100 Benevento, 5 Institute of Biomembranes and Bioenergetics, National Research Council, 70126 Bari, 6 National Institute of Biostructures and Biosystems, 00136 Rome and 7 Center of Excellence in Genomics for Biomedicine and Agri-food (CEGBA), University of Bari, 70126 Bari, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mariangela","family":"Santorsola","sequence":"additional","affiliation":[{"name":"1 Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, 2 Department of Biosciences, University of Milan, 20133 Milan, 3 Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, 70126 Bari, 4 Department of Sciences and Technologies, University of Sannio, 82100 Benevento, 5 Institute of Biomembranes and Bioenergetics, National Research Council, 70126 Bari, 6 National Institute of Biostructures and Biosystems, 00136 Rome and 7 Center of Excellence in Genomics for Biomedicine and Agri-food (CEGBA), University of Bari, 70126 Bari, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cristiano","family":"Gutt\u00e0","sequence":"additional","affiliation":[{"name":"1 Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, 2 Department of Biosciences, University of Milan, 20133 Milan, 3 Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, 70126 Bari, 4 Department of Sciences and Technologies, University of Sannio, 82100 Benevento, 5 Institute of Biomembranes and Bioenergetics, National Research Council, 70126 Bari, 6 National Institute of Biostructures and Biosystems, 00136 Rome and 7 Center of Excellence in Genomics for Biomedicine and Agri-food (CEGBA), University of Bari, 70126 Bari, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Giuseppe","family":"Gasparre","sequence":"additional","affiliation":[{"name":"1 Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, 2 Department of Biosciences, University of Milan, 20133 Milan, 3 Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, 70126 Bari, 4 Department of Sciences and Technologies, University of Sannio, 82100 Benevento, 5 Institute of Biomembranes and Bioenergetics, National Research Council, 70126 Bari, 6 National Institute of Biostructures and Biosystems, 00136 Rome and 7 Center of Excellence in Genomics for Biomedicine and Agri-food (CEGBA), University of Bari, 70126 Bari, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ernesto","family":"Picardi","sequence":"additional","affiliation":[{"name":"1 Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, 2 Department of Biosciences, University of Milan, 20133 Milan, 3 Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, 70126 Bari, 4 Department of Sciences and Technologies, University of Sannio, 82100 Benevento, 5 Institute of Biomembranes and Bioenergetics, National Research Council, 70126 Bari, 6 National Institute of Biostructures and Biosystems, 00136 Rome and 7 Center of Excellence in Genomics for Biomedicine and Agri-food (CEGBA), University of Bari, 70126 Bari, Italy"},{"name":"1 Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, 2 Department of Biosciences, University of Milan, 20133 Milan, 3 Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, 70126 Bari, 4 Department of Sciences and Technologies, University of Sannio, 82100 Benevento, 5 Institute of Biomembranes and Bioenergetics, National Research Council, 70126 Bari, 6 National Institute of Biostructures and Biosystems, 00136 Rome and 7 Center of Excellence in Genomics for Biomedicine and Agri-food (CEGBA), University of Bari, 70126 Bari, Italy"},{"name":"1 Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, 2 Department of Biosciences, University of Milan, 20133 Milan, 3 Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, 70126 Bari, 4 Department of Sciences and Technologies, University of Sannio, 82100 Benevento, 5 Institute of Biomembranes and Bioenergetics, National Research Council, 70126 Bari, 6 National Institute of Biostructures and Biosystems, 00136 Rome and 7 Center of Excellence in Genomics for Biomedicine and Agri-food (CEGBA), University of Bari, 70126 Bari, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Graziano","family":"Pesole","sequence":"additional","affiliation":[{"name":"1 Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, 2 Department of Biosciences, University of Milan, 20133 Milan, 3 Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, 70126 Bari, 4 Department of Sciences and Technologies, University of Sannio, 82100 Benevento, 5 Institute of Biomembranes and Bioenergetics, National Research Council, 70126 Bari, 6 National Institute of Biostructures and Biosystems, 00136 Rome and 7 Center of Excellence in Genomics for Biomedicine and Agri-food (CEGBA), University of Bari, 70126 Bari, Italy"},{"name":"1 Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, 2 Department of Biosciences, University of Milan, 20133 Milan, 3 Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, 70126 Bari, 4 Department of Sciences and Technologies, University of Sannio, 82100 Benevento, 5 Institute of Biomembranes and Bioenergetics, National Research Council, 70126 Bari, 6 National Institute of Biostructures and Biosystems, 00136 Rome and 7 Center of Excellence in Genomics for Biomedicine and Agri-food (CEGBA), University of Bari, 70126 Bari, Italy"},{"name":"1 Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, 2 Department of Biosciences, University of Milan, 20133 Milan, 3 Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, 70126 Bari, 4 Department of Sciences and Technologies, University of Sannio, 82100 Benevento, 5 Institute of Biomembranes and Bioenergetics, National Research Council, 70126 Bari, 6 National Institute of Biostructures and Biosystems, 00136 Rome and 7 Center of Excellence in Genomics for Biomedicine and Agri-food (CEGBA), University of Bari, 70126 Bari, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marcella","family":"Attimonelli","sequence":"additional","affiliation":[{"name":"1 Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, 2 Department of Biosciences, University of Milan, 20133 Milan, 3 Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, 70126 Bari, 4 Department of Sciences and Technologies, University of Sannio, 82100 Benevento, 5 Institute of Biomembranes and Bioenergetics, National Research Council, 70126 Bari, 6 National Institute of Biostructures and Biosystems, 00136 Rome and 7 Center of Excellence in Genomics for Biomedicine and Agri-food (CEGBA), University of Bari, 70126 Bari, 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