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   -d INT Number of threads [1]
   -c     Output a FASTA file of concatenated alleles and unknown sequences 
   -y     Output a phylip file of concatenated alleles and unknown sequences
   -o STR Output directory [.]
   -a     Print out all available MLST databases and exit
   -h     Print this message and exit
   -v     Print version number and exit
```

# Input format
The input files must be in [FASTA format](https://en.wikipedia.org/wiki/FASTA_format) and contain nucleotide sequences. These can be full genome sequences, fragmented _de novo_ assemblies or individual genes. If the gene is truncated or split over 2 ...

# Outputs

## mlst_results.allele.csv
This is a tab separated spreadsheet containing the ST number of each input FASTA file and the corresponding allele numbers for each gene in the scheme. If one of the alleles is not contained in the database, then it will be flagged with 'U' and the 3...

Isolate | ST  |"New ST" |Contamination     | aroC | dnaN | hemD | hisD | purE | sucA | thrA
------- | --- | --------|------------------|------|------|------|------|------|------|-----
sample1 | ~559| Unknown |                  | 130  | 97   | 25   | 125  | U    | 9    | 101
sample2 | 518 |         |                  | 101  | 41   | 40   | 184  | 76   | 90   | 3