include SNP-based classification of M. chimaera outbreak strain

[mdiricks]

and output it in results file per sample and summary file (e.g. "Closely related to Outbreak strain", output = strain name)

[jodyphelan]

Is there a reference for the outbreak strain and have the associated snps already been found?

[mdiricks]

Hi Jody!

Is there a reference for the outbreak strain and have the associated snps already been found?
vanIngen2017_mchimaera_outbreak.pdf
vanIngen2017_mchimaera_outbreak_supplement.pdf
-->
The SNPs for classification are on page 23 of the attached supplementary file. There are usually two SNPs per group and both should be used for correct classification. The scheme is also hierarchical, meaning group 1.1 is a subgroup of group 1.

The reference genome used is one we sequenced ourselves, it's the type strain but the genome is much better than the other version in the databases:
https://www.ncbi.nlm.nih.gov/nuccore/CP015272.1/

Greetings,
Margo

[jodyphelan]

Perfect thanks!