haansi/mtdna-server-workflow

The new mtDNA-Server workflow

mtDNA Server Workflow

This repository includes the new mtDNA-Server workflow from BAM files to homoplasmies/heteroplasmies. All steps are executed locally.

Run mtDNA-Server workflow locally

1. Install Cloudgene with the following commands

mkdir cloudgene
cd cloudgene
curl -s install.cloudgene.io | bash

2. Install the mtDNA Server workflow

./cloudgene gh seppinho/mtdna-server-workflow@latest

3. Start the local web service

./cloudgene server

4. Open your web browser and enter http://localhost:8082. Use admin and admin1978 to login.

Workflow steps

Currently the following steps are included:

• Create homplasmies/heteroplasmies with https://github.com/seppinho/mutation-server
• Calculate haplogroups with http://haplogrep.uibk.ac.at/
• Check Contamination with https://github.com/haansi/mitolib