mtDNA-Server 2: advancing mitochondrial DNA analysis through highly parallelized data processing and interactive analytics.

Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN: 1362-4962 (Electronic) Linking ISSN: 03051048 NLM ISO Abbreviation: Nucleic Acids Res Subsets: MEDLINE

Publication: 1992- : Oxford : Oxford University Press
Original Publication: London, Information Retrieval ltd.

DNA, Mitochondrial*/genetics ; Software*; Humans ; Sequence Analysis, DNA/methods ; Genome, Mitochondrial ; Workflow ; High-Throughput Nucleotide Sequencing/methods ; Internet ; Reproducibility of Results ; INDEL Mutation

Over the past decade, mtDNA-Server established itself as one of the most widely used variant calling web-services for human mitochondrial genomes. The service accepts sequencing data in BAM format and returns an annotated variant analysis report for both homoplasmic and heteroplasmic variants. In this work we present mtDNA-Server 2, which includes several new features highly requested by the community. Most importantly, it includes (a) the integration of a novel variant calling mode that accurately call insertions, deletions and single nucleotide variants at once, (b) the integration of additional quality control and input validation modules, (c) a method to estimate the required coverage to minimize false positives and (d) an interactive analytics dashboard. Furthermore, we migrated the complete analysis workflow to the Nextflow workflow manager for improved parallelization, reproducibility and local execution. Recognizing the importance of insertions and deletions as well as offering novel quality control, validation and reporting features, mtDNA-Server 2 provides researchers and clinicians a new state-of-the-art analysis platform for interpreting mitochondrial genomes. mtDNA-Server 2 is available via mitoverse, our analysis platform that offers a centralized place for mtDNA analysis in the cloud. The web-service, source code and its documentation are freely accessible at https://mitoverse.i-med.ac.at.
(© The Author(s) 2024. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Nat Rev Genet. 2015 Sep;16(9):530-42. (PMID: 26281784)
Nature. 2024 Mar;627(8003):340-346. (PMID: 38374255)
Nature. 2023 Aug;620(7975):839-848. (PMID: 37587338)
Proc Natl Acad Sci U S A. 2014 Jul 22;111(29):10654-9. (PMID: 25002485)
Genome Res. 2022 Mar;32(3):569-582. (PMID: 35074858)
Front Oncol. 2019 Sep 04;9:851. (PMID: 31552176)
Nucleic Acids Res. 2012 Oct;40(18):e137. (PMID: 22649055)
Bioinformatics. 2016 Oct 1;32(19):3047-8. (PMID: 27312411)
Nucleic Acids Res. 2021 Jan 8;49(D1):D1282-D1288. (PMID: 33300029)
BMC Bioinformatics. 2012 Aug 13;13:200. (PMID: 22888776)
Front Genet. 2022 May 19;13:887644. (PMID: 35664331)
Int J Mol Sci. 2021 Jan 19;22(2):. (PMID: 33477827)
Nucleic Acids Res. 2016 Jul 8;44(W1):W64-9. (PMID: 27084948)
Front Genet. 2022 Mar 08;13:692257. (PMID: 35350246)
Nat Commun. 2023 Aug 19;14(1):5058. (PMID: 37598215)
NAR Genom Bioinform. 2022 May 17;4(2):lqac034. (PMID: 35591888)
Nucleic Acids Res. 2023 Jul 5;51(W1):W263-W268. (PMID: 37070190)
Genome Res. 2021 Feb;31(2):309-316. (PMID: 33452015)
Cell. 2022 Sep 1;185(18):3426-3440.e19. (PMID: 36055201)
Annu Rev Genet. 2005;39:359-407. (PMID: 16285865)
Nucleic Acids Res. 2014 Nov 10;42(20):12640-9. (PMID: 25348406)
Nat Biotechnol. 2017 Apr 11;35(4):316-319. (PMID: 28398311)
Crit Rev Biochem Mol Biol. 2021 Oct;56(5):510-525. (PMID: 34120542)

Medical University of Innsbruck

0 (DNA, Mitochondrial)

Date Created: 20240506 Date Completed: 20240704 Latest Revision: 20240706

20240706

PMC11223783

10.1093/nar/gkae296

38709886