Skip to content
mtDNA contamnation detection for whole genome and targed mtDNA sequencing studies.
HTML Java R Shell
Branch: master
Clone or download
Latest commit 27a5c9f Aug 26, 2019
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
.settings Add Input Validation Nov 29, 2018
files
paper-data
resources
src
test-data/contamination
.classpath
.gitignore
.project Rename repository to haplocheck Jan 26, 2019
.travis.yml
LICENSE Create LICENSE Aug 20, 2019
README.md
pom.xml

README.md

Haplocheck

Build Status

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 haplocheck@1.0.5 --files <input-files> --output <out-folder>  

Run Haplocheck as a cloud service

Haplocheck is a contamination tool using the mtDNA phylogeny and has been integrated into the mitoverse mtDNA platform based on Cloudgene.

Haplocheck Documentation

Documentation can be found here.

Testdata

The 1000 Genomes Phase3 file analyzed with mutserve can be found here.

Blog

Check out our blog regarding mtDNA topics.

Contact

See here.

You can’t perform that action at this time.