genomicepidemiology/mlst repository overview

The MLST service contains one python script mlst.py which is the script of the latest version of the MLST service. The method enables investigators to determine the ST based on WGS data.

This repository contains the Docker image for our MLST service

See the source code repository for more details. https://bitbucket.org/genomicepidemiology/mlst/⁠

⁠Installation

docker image pull genomicepidemiolog/mlst docker tag genomicepidemiology/mlst mlst

⁠Test Example

docker run --rm -it --entrypoint=/test/test.sh mlst

⁠Usage Example

docker run --rm -it -v $MLST_DB:/database -v $(pwd):/workdir mlst -i [INPUTFILE] -o . -s [SPECIES] [-x]

See bitbucket repository for more information on how to download KMA and the MLST database

⁠Source Code Repository

https://bitbucket.org/genomicepidemiology/mlst⁠

⁠Webserver Implementation

https://cge.cbs.dtu.dk/services/mlst/⁠

⁠License

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0⁠

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.