Hello Hive mind,

I know it's the weekend and all but I'm going to try anyway. Earlier I posted about sequencing several strep suis genomes and had issues with alignment. I got some good advice to use Mauve which helped a lot still not done with it and I need to go and update that post as well. Anyway, I also ran the trimmed reads for MLST testing using SRST2, worked great all of them returned a profile and the program ran like you would expect. However I'm a little confused on the output and what it means.

I got 3 MLST profiles from 4 genomes two are identical and are a "close match" to ST 738 and the other 2 are not in the data set from PubMLST. So here are my questions.

1. Is a "close match" or "closest match" consider the same ST profile? I would have thought if there are SNPs or Indels that the would cause it to be a new ST. What is the level of change a specific gene can contain before it's a new ST?

2. Is finding a new profile something that should be expected or is it a red flag? I understand that we are going to find new profiles from time to time as the data sets grow but it feels iffy to grab 2 new STs from the start.

So there are my musing, thank you in advance for any advice or good MLST references you send my way.

Happy weekend and Cheers,

Sean