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+pMLST
+===================
+
+Plasmid Multi-Locus Sequence Typing
+
+
+Documentation
+=============
+
+The pMLST service contains one python script *pmlst.py* which is the script of the latest
+version of the pMLST service. The method enables investigators to determine the ST based on WGS data.
+
+## Content of the repository
+1. pmlst.py     - the program
+2. README.md
+3. Dockerfile   - dockerfile for building the pmlst docker container
+4. test.fsa     - test fasta file
+
+
+## Installation
+
+Setting up pMLST program
+```bash
+# Go to wanted location for pmlst
+cd /path/to/some/dir
+# Clone and enter the pmlst directory
+git clone https://bitbucket.org/genomicepidemiology/pmlst.git
+cd pmlst
+```
+
+Build Docker container
+```bash
+# Build container
+docker build -t pmlst .
+```
+
+#Download and install pMLST database
+```bash
+# Go to the directory where you want to store the pmlst database
+cd /path/to/some/dir
+# Clone database from git repository (develop branch)
+git clone https://bitbucket.org/genomicepidemiology/pmlst_db.git
+cd pmlst_db
+pMLST_DB=$(pwd)
+# Install pMLST database with executable kma_index program
+python3 INSTALL.py kma_index
+```
+
+If kma_index has not bin install please install kma_index from the kma repository:
+https://bitbucket.org/genomicepidemiology/kma
+
+## Dependencies
+In order to run the program without using docker, Python 3.5 (or newer) should be installed along with the following versions of the modules (or newer).
+
+#### Modules
+- cgecore 1.5.5
+- tabulate 0.7.7
+
+Modules can be installed using the following command. Here, the installation of the module cgecore is used as an example:
+```bash
+pip3 install cgecore
+```
+#### KMA and BLAST
+Additionally KMA and BLAST version 2.8.1 or newer should be installed.
+The newest versions of KMA and BLAST can be installed from here:
+```url
+https://bitbucket.org/genomicepidemiology/kma
+```
+
+```url
+ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
+```
+
+## Usage
+
+The program can be invoked with the -h option to get help and more information of the service.
+Run Docker container
+
+
+```bash
+# Run pmlst container
+docker run --rm -it \
+       -v $pMLST_DB:/database \
+       -v $(pwd):/workdir \
+       pmlst -i [INPUTFILE] -o . -s [SCHEME] [-x] [-mp] [-p] [-t]
+```
+
+When running the docker file you have to mount 2 directory: 
+ 1. pmlst_db (pMLST database) downloaded from bitbucket
+ 2. An output/input folder from where the input file can be reached and an output files can be saved. 
+Here we mount the current working directory (using $pwd) and use this as the output directory, 
+the input file should be reachable from this directory as well.
+ 
+` -i INPUTFILE	input file (fasta or fastq) relative to pwd `
+
+` -s SCHEME 	pMLST scheme to be used, details are in config file `
+
+` -o OUTDIR	outpur directory relative to pwd `
+
+` -x 		extended output. Will create an extented output `
+
+` -mp METHOD_PATH	Path to executable of the method to be used (kma or blast)`
+
+` -p DATABASE	Path to database directory `
+
+` -t TMP_DIR	Temporary directory for storage of results from external software. `
+
+
+## Web-server
+
+A webserver implementing the methods is available at the [CGE website](http://www.genomicepidemiology.org/) and can be found here:
+https://cge.cbs.dtu.dk/services/pMLST/
+
+Citation
+=======
+
+When using the method please cite:
+
+PlasmidFinder and pMLST: in silico detection and typing of plasmids.
+Carattoli A, Zankari E, Garcia-Fernandez A, Volby Larsen M, Lund O, Villa L, Aarestrup FM, Hasman H.
+Antimicrob. Agents Chemother. 2014. April 28th.
+[Epub ahead of print]
+
+References
+=======
+
+1. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. BLAST+: architecture and applications. BMC Bioinformatics 2009; 10:421. 
+2. Clausen PTLC, Aarestrup FM, Lund O. Rapid and precise alignment of raw reads against redundant databases with KMA. BMC Bioinformatics 2018; 19:307. 
+
+License
+=======
+
+Copyright (c) 2014, Ole Lund, Technical University of Denmark
+All rights reserved.
+
+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.