get_genus_vfdb

Short Read Sequence Typing for Bacterial Pathogens

Install

All systems
curl cmd.cat/get_genus_vfdb.sh
Debian Debian
apt-get install srst2
Ubuntu
apt-get install srst2
image/svg+xml Kali Linux
apt-get install srst2
Windows (WSL2)
sudo apt-get update sudo apt-get install srst2
Dockerfile
dockerfile.run/get_genus_vfdb

srst2

Short Read Sequence Typing for Bacterial Pathogens

This program is designed to take Illumina sequence data, a MLST database and/or a database of gene sequences (e.g. resistance genes, virulence genes, etc) and report the presence of STs and/or reference genes.