mtDNA-Server 2 is a Nextflow DSL2 pipeline to accurately detect heteroplasmic and homoplasmic variants in mitochondrial (mtDNA) genomes, details can be found in our NAR publication.
The documentation can be accessed here.
Weissensteiner H*, Forer L*, Kronenberg F, Schönherr S. mtDNA-Server 2: advancing mitochondrial DNA analysis through highly parallelized data processing and interactive analytics. Nucleic Acids Res. 2024 May 6:gkae296. doi: 10.1093/nar/gkae296. Epub ahead of print. PMID: 38709886.
Release v2.1.15 - Add option for min mean coverage
Release v2.1.14 - Load resource conf
Release v2.1.13 - Update to latest Haplogrep3
Release v2.1.12 - Install Haplogrep3 tree directly.
Release v2.1.11 - Improve QC command, update to latest mutserve v2.0.1.
Release v2.1.10 - Improved mutect2 support: create missing RG tags, write inidividual reference sequence on the fly, support complex ref tags.