bioedge/reference-based_assembly repository overview

Docker container with installation of reference-based_assembly that is ready to use.

The pipeline is installed into the /opt/reference-based_assembly folder and ensure the reference-based_assembly command in the path.

⁠Usage

You can download and run this image using the following commands:

docker pull bioedge/reference-based_assembly
docker run --rm -v /host/data:/data bioedge/reference-based_assembly consensus_fasta.py -h

• The -v /host/data:/data mounts the host folder /host/data into container's /data directory.
• In some cases, you need to set the directory into 0777 mode. Please try opening up the directory permission if you run into trouble.

⁠Example

⁠The fastq files, reference file are in /host/data/test

• R1.fastq
• R2.fastq
• reference.fasta

⁠Run reference-based_assembly in the container

$ docker run --rm -v  /host/data/test:/data bioedge/reference-based_assembly consensus_fasta.py -r reference.fasta \
-1 R1.fastq -2 R2.fastq -o TestOutput --temp docker_testing \
--procs 4 

⁠Output

• TestOutput.fasta
• TestOutput.changelog

⁠Contact

• [email protected]⁠