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Ultrafast sequence typing and gene detection from NGS raw reads
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README.md

STing

Table of contents:

Documentation

Documentation Status
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

wget https://github.com/jordanlab/STing/releases/download/1.0.0/sting_v1.0.0.tar.gz
tar xfv sting_v1.0.0.tar.gz
export PATH=$PWD/sting:$PATH

From source:

./autogen.sh
./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:

mkdir STing_demo
cd STing_demo

Downloading the Neisseria spp. MLST database from PubMLST.org and build a STing index from it:

db_util.py fetch --query "Neisseria spp." --out_dir my_dbs --build_index

Downloading a WGS sample to analyze:

wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR026/ERR026529/ERR026529_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR026/ERR026529/ERR026529_2.fastq.gz

Run STing typer:

typer -x my_dbs/neisseria_spp/db/index -1 ERR026529_1.fastq.gz -2 ERR026529_2.fastq.gz -s ERR026529 -c -a -d -t ERR026529.depth.tsv -y -o ERR026529.results.tsv --sensitive

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:

indexer -h
typer -h
detector -h
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