Skip to content

Commit

Permalink
Remove danger sign from query assign docs
Browse files Browse the repository at this point in the history
Now that website updated
  • Loading branch information
johnlees committed Dec 16, 2021
1 parent 9067f4c commit 8b13e45
Showing 1 changed file with 7 additions and 7 deletions.
14 changes: 7 additions & 7 deletions docs/query_assignment.rst
Original file line number Diff line number Diff line change
Expand Up @@ -3,12 +3,6 @@ Query assignment
This is the recommended mode to use PopPUNK, as long as a database is available for
your species. If there is no database available, you can fit your own (:doc:`model_fitting`).

.. danger::
Most reference databases available below are for a previous version of PopPUNK.
Please bear with us as we update this, more reference databases which work
with version 2 of PopPUNK will be released shortly. You can still fit your
own model to your data.

Briefly, `download your reference database <https://poppunk.net/pages/databases.html>`__ and run::

poppunk_assign --db database --query qfile.txt \
Expand All @@ -21,6 +15,12 @@ Downloading a database
----------------------
Current PopPUNK databases can be found here: https://poppunk.net/pages/databases.html

.. information::
We currently only have three reference databases available for public use.
Please bear with us as we update this, more reference databases which work
with version 2 of PopPUNK will be released shortly. You can still fit your
own model to your data.

We refer to sequences in the database as references, and those being added
as queries. The clusters assigned by PopPUNK are variable-length-k-mer clusters (VLKCs).

Expand Down Expand Up @@ -240,4 +240,4 @@ depending on whether they were a query or reference input.
each time it is called. If your query set is large and you want repeated visualisations,
run ``poppunk_assign`` with ``--update-db``.

See :doc:`visualisation` for more details.
See :doc:`visualisation` for more details.

0 comments on commit 8b13e45

Please sign in to comment.