STing
Table of contents:
- Documentation
- Requirements
- Installation
- Quickstart guide
- Typing
- Gene detection
- Preparing the database:
- STing applications
Documentation
See the full documentation at: https://sting.readthedocs.io/
Requirements
- Linux OS
- gcc >= 4.8 and gcc <= 5.3
You may use gcc >= 5.3 to compile STing but you will see multiple warning messages. Those warning messages will not interfere with the binary generation. - autotols (Ubuntu: autotools)
- Autoconf >= 2.69
- Automake >= 1.15.1
- Libtool >= 2.4.6
- autotools developer headers (Ubuntu: autotools-dev)
- zlib >= 1.2.8 (Ubuntu: zlib)
- zlib developer headers (Ubuntu: zlib1g-dev)
Installation
Using the pre-built static binaries
tar xfv STing_v1.0.1.tar.gz
wget https://github.com/jordanlab/STing/raw/master/scripts/db_uti l.py -O STing/db_util.py
chmod +x STing/db_util.py
export PATH=$PWD/STing:$PATH
From source:
./configure
make
make install
By default, make install will install all the files in /usr/local/bin, /usr/local/lib etc. You can specify an installation prefix other than /usr/local using the --prefix options from ./configure, for instance ./configure --prefix=$HOME. Please check all the available options of ./configure by executing ./configure --help.
Quickstart guide
Pre-built MLST databases
Pre-built MLST databases are provided here and updated weekly: https://github.com/jordanlab/STing_datasets
We recommend building a new database each time STing is run, or daily if under continual use, to ensure the most up to date definitions as possible
Typing
Preparing directory:
cd STing_demo
Downloading the Neisseria spp. MLST database from PubMLST.org and build a STing index from it:
Downloading a WGS sample to analyze:
Run STing typer:
STing applications
STing has three applications:
-
indexer: Creates the indexes (databases) required to execute a locus-based typing analysis and detect genes. -
typer: Predicts STs of a read sample based on an index built from a species-specific locus-based typing scheme (allelic profile table and sequences of observed alleles). -
detector: Detects genes in a read sample based on an index built from sequences of a set of genes of interest.
To explore the usage and available options for each tool, run the corresponding application using the option -h or --help:
typer -h
detector -h