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

Gene detection

Prbuilt CARD and VFDB databases are available on the STing Datasets repository: https://github.com/jordanlab/STing_datasets
Both pre-built databases and the one described below are for use with detector.

Preparing directory:

mkdir -p STing_demo/my_dbs/card
cd STing_demo/my_dbs/card

Preparing the database:

Downloading the antimicrobial resistance gene database from CARD

wget https://card.mcmaster.ca/latest/data -O card.tgz
tar xvf card.tgz

Changing IUPAC extended DNA characters to N on the CARD nucleotide file:

sed -e '/^[^>]/s/[^ATGCatgc]/N/g' nucleotide_fasta_protein_homolog_model.fasta > card.fasta

Creating STing db config file:

echo -e "[loci]\ncard\tcard.fasta\n" > config.txt

The new config file should look like this:

[loci]
card    card.fasta

Creating the STing database index:

indexer -c config.txt -p db/index -m GDETECT

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 detector:

cd ../../
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