Docker image with SISTR command line software (GitHub page).
SISTR: Salmonella serovar predictions from whole-genome sequence assemblies
You can download and run this image using the following commands:
# Get Docker image
docker pull ummidock/sistr_cmd:1.0.2
# Run sistr_cmd
docker run --rm -u $(id -u):$(id -g) -it -v /local/folder/data:/data/ ummidock/sistr_cmd:1.0.2 sistr --qc -vv --alleles-output /data/allele-results.json --novel-alleles /data/novel-alleles.fasta --cgmlst-profiles /data/cgmlst-profiles.csv -f tab -o /data/sistr-output.tab /data/assembly.fasta
This Docker image contains:
- sistr_cmd
- Blast+
- MAFFT
- Mash