Search MLST profile of a strain

Similarly to wgMLST analysis, you need a draft genome or raw reads data to find the MLST profile.

Note

You can perform MLST searches on multiple genomes or raw reads simultaneously.

Genome data

You can search ST from GENOME fasta sequence files.

claMLST search --help
Usage: claMLST search [OPTIONS] DATABASE GENOMES

Searches ST number for assembly GENOMES using an mlst DATABASE

Options:
-i, --identity FLOAT   Minimum identity to search gene (default=0.9)
-c, --coverage FLOAT   Minimum coverage to search gene (default=0.9)
-f, --fasta FILENAME   Writes fasta file with gene allele
-o, --output FILENAME  Writes ST search result to (default:stdout)

Reads data

Alternatively, you can search ST directly from raw reads with single or paired FASTQS(.gz) files.

claMLST search2 --help
Usage: claMLST search2 [OPTIONS] DATABASE [FASTQS]...

Searches ST number from FASTQS(.gz) raw reads using an mlst DATABASE.

Options:
-i, --identity FLOAT   Minimum identity to search gene (default=0.9).
-c, --coverage FLOAT   Minimum coverage to search gene (default=0.95).
-r, --reads INTEGER    Minimum reads coverage to search gene (default=10).
--paired / --single    Defines type of fastqs files.
-f, --fasta FILENAME   Writes fasta file with gene allele.
-o, --output FILENAME  Writes ST search result to (default:stdout).

Note

The default identity and coverage thresholds are set to 0.9 and can be modulated using the -i and -c options.

Note

If new alleles are present, you can obtain their sequences with the -f option.