Y24-170 - Link dual index tag groups

[KatyTaylor]

Background - science of tags
Tag plates are plates that contain small DNA sequences called tags (or barcodes, indexes...). The contents of these plates are added to samples in order to create libraries that can be sequenced.

Dual index tags are ones where a sample will be linked to two tags, called 'i7' and 'i5' (refers to the direction you're reading the DNA molecule), or sometimes referred to in Sequencescape as 'tag1' and 'tag2'.

In dual index tag plates, both i7 and i5 oligos are in the same well. i.e. well 'A1' will contain both an i7 and an i5 tag; B1 will contain 2 different ones, etc. They are always combined in the well - they don't come separately.

Background - tags in Sequencescape & Limber

Sequencescape represents dual index tag groups as 2 separate tag groups - one that contains the i7 tags, and one that contains the i5 tags. For example, see the following:

• https://training.sequencescape.psd.sanger.ac.uk/tag_groups/227 (i7)
• https://training.sequencescape.psd.sanger.ac.uk/tag_groups/228 (i5)

Tag groups are used in two features in Sequencescape:

1. When creating libraries in SeqOps, using Limber - see screenshot of page here
2. When importing ready-made libraries, using the Chromium library plate manifest

On the tagging screen linked above, there are two ways of selecting which tags you want. One is to scan a barcode on the actual physical tag plate you're using - see the 'Tag Plate' box. The other is to select the i7 and i5 tag groups that you are using - see the dropdowns further down.

Research questions

1. Is there any reason from a user point of view why there should be two tag group dropdowns instead of one, in the above mentioned tagging screen? This is a question for the lab users. Not sure who best to ask, but I think I have talked to Matt J (former bespoke team) about using this screen in the past - maybe a good place to start. Also, Matthew M, Sara W, and Jamie L.
2. If answer to above is no, come up with a design for a combined i7 & i5 dual index tag group - either linking together the existing tag groups (using something more robust than the name), or creating a new model. It should be able to be used in the existing contexts:
   • replacing the two dropdowns on that tagging screen with one
   • in a new manifest type, similar to Chromium library plate manifest but for dual index tags, as described in Y24-055 New plate manifest type in SS to reduce the number of incorrect tags #4083
   • tag groups are also linked behind the scenes to tag layout templates - see ERD here - this is involved when creating tag plates using Gatekeeper.

Who the primary contacts are for this work
Katy (PSD), Rich C (SSR)

References:

• Y24-055 New plate manifest type in SS to reduce the number of incorrect tags
• Y24-218 - Create a new tag set model to link tag groups
• Y24-219 - Link tag groups with tag sets
  Y24-220 - Create API V2 end point for tag sets
• Y24-221 - Create Sequencescape pages for tag sets
  Y24-222 - Select tag set in Limber tagging screen instead of tag groups
  Y24-231 - UAT Action to link tag groups with a tag set

We will start with the first 3 story to be able to implement the dual index manifests and it will play a role of investigating later stories.

Y24-221 is the next important story to allow user to make their own tag group links (It should be limited to SSRs and admin role).

Rich will give us an Initial list of tag groups to link.