Haplocheck is a software that leverages the mitochondrial phylogeny to detect contamination in mtDNA sequencing studies and in whole genome sequencing studies. We provide haplocheck as a standalone pipeline for local usage and as a cloud web service (via https://mitoverse.i-med.ac.at).
Run Haplocheck locally
Using Cloudgene, the complete workflow can also be executed locally. The final HTML report is located at
<out-folder>/report. Haplocheck requires Java 8 or higher.
curl -s install.cloudgene.io | bash -s 2.0.0-rc14 ./cloudgene install https://github.com/genepi/haplocheck/releases/download/v1.0.5/haplocheck.zip ./cloudgene run email@example.com --files <input-files> --output <out-folder>
Run Haplocheck as a cloud service
Documentation can be found here.
The 1000 Genomes Phase3 file analyzed with mutserve can be found here.
Check out our blog regarding mtDNA topics.