mtDNA-Server statistics

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Citations per year

Number of citations per year for the bioinformatics software tool mtDNA-Server

Tool usage distribution map

This map represents all the scientific publications referring to mtDNA-Server per scientific context
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mtDNA-Server specifications


Unique identifier OMICS_12341
Name mtDNA-Server
Interface Web user interface
Restrictions to use None
Input format FASTQ,BAM
Output data An interactive HTML report summarizing all findings, the detected heteroplasmic and homoplasmic sites, the HaploGrep input and final classification file and the raw pileup file including base position counts per sample.
Computer skills Basic
Version 1.0.7
Stability Stable
Maintained Yes





  • person_outline Sebastian Schönherr

Publication for mtDNA-Server

mtDNA-Server citations


Whole genome sequencing for an enhanced understanding of genetic variation among South Africans

Nat Commun
PMCID: 5727231
PMID: 29233967
DOI: 10.1038/s41467-017-00663-9

[…] Haplogrep2 was used to identify mitochondrial haplotypes for each individual. For this, all reads were aligned using BWA-mem to the RSRS sequence. The BAM files produced were then uploaded to mtDNA-server service as suggested by the webserver documentation. This service performs QC filtering (Mapping Quality Score < 20; read alignment quality < 30; base quality < 20; heteroplasmy level < 1 […]


The population genomics of archaeological transition in west Iberia: Investigation of ancient substructure using imputation and haplotype based methods

PLoS Genet
PMCID: 5531429
PMID: 28749934
DOI: 10.1371/journal.pgen.1006852

[…] ambridge Reference Sequence (rCRS; NC_012920.1) [], trimming low quality bases (q ≥ 20) and filtering by mapping quality (q ≥ 30) and duplicate reads as above. mtDNA haplogroups were identified using mtDNA-server (, with default parameters. […]


A novel but frequent variant in LPA KIV 2 is associated with a pronounced Lp(a) and cardiovascular risk reduction

Eur Heart J
PMCID: 5837733
PMID: 28444229
DOI: 10.1093/eurheartj/ehx174
call_split See protocol

[…] action of NGS reads. Data analysis was therefore performed by aligning all reads to one single kringle repeat and low-level variants were called using the highly specific mutation detection pipeline ‘mtDNA-Server’ with slight adaptions (, 25 March 2017) (see ). The LPA KIV-2 specific variant calling pipeline will be available at, 25 March 2017 […]


Entire Mitochondrial DNA Sequencing on Massively Parallel Sequencing for the South Korean Population

PMCID: 5334155
PMID: 28244283
DOI: 10.3346/jkms.2017.32.4.587
call_split See protocol

[…] d HaploGrep2 (25; according to the PhyloTree Build 16 database (26; Van Oven et al. 2009). mtDNA MPS raw data in Binary Alignment/Map (BAM) format were also loaded on the mtDNA-Server (27; available at in order to investigate the heteroplasmic variants and confirm the data quality. […]


Experiences with workflows for automating data intensive bioinformatics

Biol Direct
PMCID: 4539931
PMID: 26282399
DOI: 10.1186/s13062-015-0071-8

[…] he research group Databases and Information Systems (DBIS) at the University of Innsbruck exists, developing data-intensive bioinformatics software solutions such as Cloudgene [], HaploGrep [] or the mtDNA-Server ( Lately, the developed workflow system Cloudgene has been utilized as the underlying architecture for the Michigan Imputation Server, developed in coopera […]


Validation of Next Generation Sequencing of Entire Mitochondrial Genomes and the Diversity of Mitochondrial DNA Mutations in Oral Squamous Cell Carcinoma

PLoS One
PMCID: 4532422
PMID: 26262956
DOI: 10.1371/journal.pone.0135643

[…] ed-end read chemistry.The paired-end fastq files from the Illumina HiSeq 2500 were analysed with our highly parallelized in-house-pipeline based on Cloudgene ([] and manuscript in preparation) called mtDNA-Server ( In a first step the data quality was controlled by creating reports in order to verify values such as the “per base sequence quality”, “per base N conten […]

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mtDNA-Server institution(s)
Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria; Department of Database and Information Systems, Institute of Computer Science, University of Innsbruck, Innsbruck, Austria; Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
mtDNA-Server funding source(s)
Supported by EU FP7 project [602133]; Austrian Science Fund (FWF) [J-3401].

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