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.
- Install the workflow engine Cloudgene
mkdir cloudgene cd cloudgene curl -s install.cloudgene.io | bash
- Install the mtDNA Server workflow
./cloudgene gh firstname.lastname@example.org -name mtdna-server-v1.1.3
Run the workflow
a. Graphical Execution
Open your web browser and navigate to http://localhost:8082. Use
b. Command line Execution
./cloudgene run mtdna-server-v1.1.3 --input apps/mtdna-server-v1.1.3/*/test-data
Currently the following steps are included: