mtDNA-Server 2

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mtdna-server-2 nf-test

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.

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Documentation

The documentation can be accessed here.

Running Pipeline Locally

git clone https://github.com/genepi/mtdna-server-2
cd mtdna-server-2
nextflow run main.nf -c tests/test_single_bam.config -profile <docker,singularity>

You can find all additional DSL2 parameters and configuration options here.

Citation

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. 52:W102-W107, 2024. PMID: 38709886

Version History

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.