Frequently Asked Question FAQ

The TYGS is currently limited to 50 genomes not because of a limitation of the method but because we have to keep an eye on the compute cluster usage. But for most use cases this limit is clearly more than enough. However, we usually offer to increase the upload cap for a given email address on TYGS beyond the default of 50 user genomes when asked for, assuming the requested upload cap is not exorbitantly high.

Before asking for an increased upload cap, please consider and prepare the following aspects though:

1. How large is your final dataset?
2. Is your dataset really final?
3. In case you want to analyze few own isolates together with a rather large list of 'reference strains' which you have obtained from some other web site:
   • Which insights do you expect to get from such an analysis?
   • Why can't you analyze your isolates through the TYGS without these 'reference strains' (also please read the FAQ item on type strains vs. 'reference strains')?
4. Have you removed redundant strains (e.g. clonal strains) from the dataset to reduce its size and, if not, why?
5. Is your dataset a rather diverse selection of strains or do the strains belong to a group of closely related strains?
6. Are your files properly labelled (e.g. labels will be shown in the trees)?
7. Does your dataset contain type-strain genomes and, if yes, why? The TYGS already provides type-strain genomes.
8. Do you want to restrict the TYGS analysis to the uploaded genome sequences or do you want to use the TYGS in standard mode (i.e. the TYGS will determine closely related type strain genomes)?

How does the procedure work?

Please use the TYGS feedback form and answer the above questions as complete as possible. Upon reception of your request, we will check it and might come back to you with further questions (basically to narrow down the computational complexity of your specific job). If everything is fine, we will set up an exception for your e-mail address which allows you to submit TYGS requests with the requested number of user sequences. Should the web server dislike a larger amount of data and produces a timeout, we can usually offer to submit the files on your behalf from within our network. In that case the file exchange can be be organized via a confidential folder on our institutional cloud.

The exception will be usually valid for a week but can normally be extended on request. Please note that your job(s) will use some resources of our in-house compute cluster. That is, please do not start multiple redundant jobs of that size if this can be avoided.