Submitting data

All data live in a database at https://github.com/lskatz/mlst-hash-template-example. The specification for how the data are formatted is at https://lskatz.github.io/mlst-hash-template-example/docs/specification.html.

Essentially, to add a new sample to the database is to make a pull request with these files.

Files to change

Your data have to be concatenated to these files.

  • refs.fasta
  • alleles.tsv
  • profiles.tsv
  • clusters.tsv

refs.fasta and alleles.tsv

This is the bare minimum. Add any new alleles to alleles.tsv. In this database, alleles are coded with md5sums.

If you have a new locus, add it to refs.fasta.

profiles.tsv

If you have samples, add them to profiles.tsv. In this database, alleles are coded with md5sums. Also in this database, there is a field with LINCode which is a nonstandard way to display the data. A future direction should be to entirely move the LINCodes to clusters.tsv.

clusters.tsv

For each sample, call the LINCode and then add that in the third field in clusters.tsv.

Pull request

Once these files are modified, make a new branch in your space, and then make a pull request from your branch to this master branch. There are some automated tests to ensure this all works and then we will manually review.