MToolBox: a highly automated pipeline for heteroplasmy annotation and prioritization analysis of human mitochondrial variants in high-throughput sequencing

Claudia Calabrese; Domenico Simone; Maria Angela Diroma; Mariangela Santorsola; Cristiano Guttà; Giuseppe Gasparre; Ernesto Picardi; Graziano Pesole; Marcella Attimonelli

doi:10.1093/bioinformatics/btu483

MToolBox: a highly automated pipeline for heteroplasmy annotation and prioritization analysis of human mitochondrial variants in high-throughput sequencing

Bioinformatics. 2014 Nov 1;30(21):3115-7. doi: 10.1093/bioinformatics/btu483. Epub 2014 Jul 14.

Authors

Claudia Calabrese¹, Domenico Simone¹, Maria Angela Diroma¹, Mariangela Santorsola¹, Cristiano Guttà¹, Giuseppe Gasparre¹, Ernesto Picardi², Graziano Pesole², Marcella Attimonelli¹

Affiliations

¹ 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.
² 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.

Abstract

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.

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.

Availability and implementation: MToolBox package is available at https://sourceforge.net/projects/mtoolbox/.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

DNA, Mitochondrial / chemistry*
Genetic Variation*
Genome, Mitochondrial*
High-Throughput Nucleotide Sequencing / methods*
Humans
Molecular Sequence Annotation
Sequence Analysis, DNA / methods*
Software*

Substances

DNA, Mitochondrial