Add strains to the database

Next, you need to iteratively add your strains to the database. You can use a draft genome (we recommend using Spades for assembly). You can also add a reference genome for comparison.

Note

You need to add each strain one by one to the database. You can specify strain name using -s option.

Genome data

You can add strains using GENOME fasta sequence file.

wgMLST add --help
Usage: wgMLST add [OPTIONS] DATABASE GENOME

Adds a strain GENOME to the wgMLST DATABASE.

Options:
-s, --strain TEXT     Name of the strain (default:genome name)
-i, --identity FLOAT  Minimum identity to search gene (default=0.95)
-c, --coverage FLOAT  Minimum coverage to search gene (default=0.9)

Reads data

Alternatively, you can also add strains from raw reads direcly with single or paired FASTQS(.gz) files.

wgMLST add2 --help
Usage: wgMLST add2 [OPTIONS] DATABASE [FASTQS]...

Adds a strain from FASTQS(.gz) reads to the wgMLST DATABASE.

Options:
-s, --strain TEXT     Name of the strain (default:genome name).
-i, --identity FLOAT  Minimum identity to search gene (default=0.95).
-c, --coverage FLOAT  Minimum coverage to search gene (default=0.9).
-r, --reads INTEGER   Minimum reads coverage to search a gene
                      (default=10).

Note

The defaut identity and coverage treshold are set to 0.9 and can be modulated with -i and -c options.

Warning

Carefully check that the allele calling has been performed correctly for each genome. Check the number of genes found for each strain using the strain command.