cg/wgMLST analysis

A workflow analysis of cg/wgMLST is performed using a series of Python scripts described below.

• Initialise a database
• Add strains to the database
• Check quality of the database
• Export results
• Export sequences
• Other analysis available

pyMLST architecture for cg/wgMLST analysis

All avalaible commands can be listed using help fonction:

wgMLST --help

Usage: wgMLST [OPTIONS] COMMAND [ARGS]...

Whole/Core genome MLST analysis.

Commands:
add            Adds a strain GENOME to the wgMLST DATABASE.
add2           Adds a strain from FASTQS(.gz) reads to the wgMLST...
create         Creates a wgMLST DATABASE from a template COREGENE.
distance       Extracts a distance matrix from a wgMLST DATABASE.
gene           Extracts a list of genes from a wgMLST DATABASE.
import         Creates a wgMLST DATABASE from an online resource.
mlst           Extracts an MLST table from a wgMLST DATABASE.
msa            Computes Multiple Sequence Alignment from a wgMLST...
recombination  Searches potential gene recombinations from wgMLST...
remove         Removes STRAINS or GENES from a wgMLST DATABASE.
sequence       Extracts sequences from a wgMLST DATABASE.
stats          Extracts stats from a wgMLST DATABASE.
strain         Extracts a list of strains from a wgMLST DATABASE.
subgraph       Searches group of strains at a DISTANCE threshold.