circlator_sanger-pathogens

docker-circlator_sanger-pathogens

Docker image with Circlator software (GitHub page).

Circlator: A tool to circularize genome assemblies

Usage

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

# Get Docker image
docker pull ummidock/circlator_sanger-pathogens:v1.5.3

# Run Circlator
## Given an assembly assembly.fasta in FASTA format and corrected PacBio reads in a file called reads, run
docker run --rm -u $(id -u):$(id -g) -it -v /local/folder/data:/data/ ummidock/circlator_sanger-pathogens:v1.5.3 circlator all /data/assembly.fasta /data/reads /data/circlator_output/

For more examples see Circlator GitHub

Image Content

This Docker image contains:

• Circlator v1.5.3
• BWA v0.7.17
• Prodigal v2.6.3
• Samtools v1.3.1
• MUMmer v4.0.0beta2
• SPAdes v3.11.1
• Canu v1.6
• Blat v36x2
• AMOS v3.1.0 (without GUI interface)