Skip to content
The new mtDNA-Server workflow
Branch: master
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
files
jars
test-data
.project
README.md
mtdna-server.yaml

README.md

mtDNA-Server Workflow

This repository includes the new mtDNA-Server workflow starting with BAM files. The workflow can be executed locally without transfering any data. For initial read mapping (FASTQ to BAM), we recommend using bwa mem.

The publicly available web service mtDNA-Server also includes read mapping.

Getting Started

The workflow outputs homoplasmic and heteroplasmic sites using Mutation-Server, haplogroups using HaploGrep and contamination using mitolib.

  1. Install the workflow engine Cloudgene
mkdir cloudgene
cd cloudgene
curl -s install.cloudgene.io | bash
  1. Install the mtDNA Server workflow
./cloudgene gh seppinho/mtdna-server-workflow@v1.1.3 -name mtdna-server-v1.1.3
  1. Run the workflow

    a. Graphical Execution

    ./cloudgene server
    

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

    b. Command line Execution

    ./cloudgene run mtdna-server-v1.1.3 --input apps/mtdna-server-v1.1.3/*/test-data
    

Workflow steps

Currently the following steps are included:

You can’t perform that action at this time.