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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.