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ummidock/sistr_cmd

By ummidock

•Updated over 8 years ago

SISTR: Salmonella serovar predictions from whole-genome sequence assemblies

Image
Machine learning & AI
Data science
0

319

ummidock/sistr_cmd repository overview

⁠docker-sistr_cmd

Docker Automated buil

Docker image with SISTR⁠ command line software (GitHub page⁠).

SISTR: Salmonella serovar predictions from whole-genome sequence assemblies

⁠Usage

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

⁠Image Content

This Docker image contains:

  • sistr_cmd
  • Blast+
  • MAFFT
  • Mash

Tag summary

Content type

Image

Digest

Size

1.2 GB

Last updated

over 8 years ago

docker pull ummidock/sistr_cmd:1.0.2