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+ − 1 pMLST
+ − 2 ===================
+ − 3
+ − 4 Plasmid Multi-Locus Sequence Typing
+ − 5
+ − 6
+ − 7 Documentation
+ − 8 =============
+ − 9
+ − 10 The pMLST service contains one python script *pmlst.py* which is the script of the latest
+ − 11 version of the pMLST service. The method enables investigators to determine the ST based on WGS data.
+ − 12
+ − 13 ## Content of the repository
+ − 14 1. pmlst.py - the program
+ − 15 2. README.md
+ − 16 3. Dockerfile - dockerfile for building the pmlst docker container
+ − 17 4. test.fsa - test fasta file
+ − 18
+ − 19
+ − 20 ## Installation
+ − 21
+ − 22 Setting up pMLST program
+ − 23 ```bash
+ − 24 # Go to wanted location for pmlst
+ − 25 cd /path/to/some/dir
+ − 26 # Clone and enter the pmlst directory
+ − 27 git clone https://bitbucket.org/genomicepidemiology/pmlst.git
+ − 28 cd pmlst
+ − 29 ```
+ − 30
+ − 31 Build Docker container
+ − 32 ```bash
+ − 33 # Build container
+ − 34 docker build -t pmlst .
+ − 35 ```
+ − 36
+ − 37 #Download and install pMLST database
+ − 38 ```bash
+ − 39 # Go to the directory where you want to store the pmlst database
+ − 40 cd /path/to/some/dir
+ − 41 # Clone database from git repository (develop branch)
+ − 42 git clone https://bitbucket.org/genomicepidemiology/pmlst_db.git
+ − 43 cd pmlst_db
+ − 44 pMLST_DB=$(pwd)
+ − 45 # Install pMLST database with executable kma_index program
+ − 46 python3 INSTALL.py kma_index
+ − 47 ```
+ − 48
+ − 49 If kma_index has not bin install please install kma_index from the kma repository:
+ − 50 https://bitbucket.org/genomicepidemiology/kma
+ − 51
+ − 52 ## Dependencies
+ − 53 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).
+ − 54
+ − 55 #### Modules
+ − 56 - cgecore 1.5.5
+ − 57 - tabulate 0.7.7
+ − 58
+ − 59 Modules can be installed using the following command. Here, the installation of the module cgecore is used as an example:
+ − 60 ```bash
+ − 61 pip3 install cgecore
+ − 62 ```
+ − 63 #### KMA and BLAST
+ − 64 Additionally KMA and BLAST version 2.8.1 or newer should be installed.
+ − 65 The newest versions of KMA and BLAST can be installed from here:
+ − 66 ```url
+ − 67 https://bitbucket.org/genomicepidemiology/kma
+ − 68 ```
+ − 69
+ − 70 ```url
+ − 71 ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
+ − 72 ```
+ − 73
+ − 74 ## Usage
+ − 75
+ − 76 The program can be invoked with the -h option to get help and more information of the service.
+ − 77 Run Docker container
+ − 78
+ − 79
+ − 80 ```bash
+ − 81 # Run pmlst container
+ − 82 docker run --rm -it \
+ − 83 -v $pMLST_DB:/database \
+ − 84 -v $(pwd):/workdir \
+ − 85 pmlst -i [INPUTFILE] -o . -s [SCHEME] [-x] [-mp] [-p] [-t]
+ − 86 ```
+ − 87
+ − 88 When running the docker file you have to mount 2 directory:
+ − 89 1. pmlst_db (pMLST database) downloaded from bitbucket
+ − 90 2. An output/input folder from where the input file can be reached and an output files can be saved.
+ − 91 Here we mount the current working directory (using $pwd) and use this as the output directory,
+ − 92 the input file should be reachable from this directory as well.
+ − 93
+ − 94 ` -i INPUTFILE input file (fasta or fastq) relative to pwd `
+ − 95
+ − 96 ` -s SCHEME pMLST scheme to be used, details are in config file `
+ − 97
+ − 98 ` -o OUTDIR outpur directory relative to pwd `
+ − 99
+ − 100 ` -x extended output. Will create an extented output `
+ − 101
+ − 102 ` -mp METHOD_PATH Path to executable of the method to be used (kma or blast)`
+ − 103
+ − 104 ` -p DATABASE Path to database directory `
+ − 105
+ − 106 ` -t TMP_DIR Temporary directory for storage of results from external software. `
+ − 107
+ − 108
+ − 109 ## Web-server
+ − 110
+ − 111 A webserver implementing the methods is available at the [CGE website](http://www.genomicepidemiology.org/) and can be found here:
+ − 112 https://cge.cbs.dtu.dk/services/pMLST/
+ − 113
+ − 114 Citation
+ − 115 =======
+ − 116
+ − 117 When using the method please cite:
+ − 118
+ − 119 PlasmidFinder and pMLST: in silico detection and typing of plasmids.
+ − 120 Carattoli A, Zankari E, Garcia-Fernandez A, Volby Larsen M, Lund O, Villa L, Aarestrup FM, Hasman H.
+ − 121 Antimicrob. Agents Chemother. 2014. April 28th.
+ − 122 [Epub ahead of print]
+ − 123
+ − 124 References
+ − 125 =======
+ − 126
+ − 127 1. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. BLAST+: architecture and applications. BMC Bioinformatics 2009; 10:421.
+ − 128 2. Clausen PTLC, Aarestrup FM, Lund O. Rapid and precise alignment of raw reads against redundant databases with KMA. BMC Bioinformatics 2018; 19:307.
+ − 129
+ − 130 License
+ − 131 =======
+ − 132
+ − 133 Copyright (c) 2014, Ole Lund, Technical University of Denmark
+ − 134 All rights reserved.
+ − 135
+ − 136 Licensed under the Apache License, Version 2.0 (the "License");
+ − 137 you may not use this file except in compliance with the License.
+ − 138 You may obtain a copy of the License at
+ − 139
+ − 140 http://www.apache.org/licenses/LICENSE-2.0
+ − 141
+ − 142 Unless required by applicable law or agreed to in writing, software
+ − 143 distributed under the License is distributed on an "AS IS" BASIS,
+ − 144 WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ − 145 See the License for the specific language governing permissions and
+ − 146 limitations under the License.
