# Genotyphi

## About Genotyphi

Genotyphi is a sequence-based typing method for Salmonella Typhi developed by Wong _et al,_ 2016, with software available from [https://github.com/katholt/genotyphi](https://github.com/katholt/genotyphi). Pathogenwatch uses an in-house implementation designed to work with assembly output rather than mapping to CT18, and has been tested to ensure it provides the same assignments.

### Genotyphi Assignment Method

1. Genotyphi SNP-containing loci are BLASTed against the assembly with:`blastn -task blastn -perc_identity 80.0 -evalue 1.0E-60 -max_target_seqs 200 -penalty -1 -reward 1`
2. For each variant location the best (highest percent identity) overlapping match is selected and the nucleotide at the variant position is noted.
3. Each variant is then compared to the diagnostic variants from the genotyphi schema, and processed according to the rules encoded in the original genotyphi script.
4. Finally the result and the number of matched sites is reported to the user. If not all sites are matched, or some sites duplicated, e.g due to contamination, it is possible that the incorrect assignment can be given.

## How to cite

If you use the output from Genotyphi please cite the references given at [https://github.com/katholt/genotyphi](https://github.com/katholt/genotyphi).



