Add iqPlaAffi

[jesgomez]

Assembly review request

• ToLID: iqPlaAffi1
• Species: Platycleis affinis
• Project: ERGA-BGE
• Affiliation: CNAG

[erga-ear-bot]

Hi @jesgomez, thanks for sending the EAR of Platycleis affinis.
I added the corresponding tag to the PR and will contact a supervisor and a reviewer ASAP.

[erga-ear-bot]

Hi @tbrown91, do you agree to supervise this assembly?
Please reply to this message only with OK to give acknowledge.

[tbrown91]

Ok

[erga-ear-bot]

*****
EAR Reviewer Selection Process
Date: 2026-02-09 17:26

All Eligible Candidates:

Github ID     | Full Name        | Institution | Total Reviews | Last Review | Active | Working PRs | Calling Score | Adjusted Score
------------------------------------------------------------------------------------------------------------------------------------
ldemirdj      | Lola Demirdjian  | Genoscope   | 15            | 2026-02-04  | Y      | 1           | 1042          | 1072          
EmilieTeo     | Emilie Teodori   | Genoscope   | 17            | 2026-02-09  | Y      | 1           | 1040          | 1070          
CaroB-M       | Caroline Menguy  | Genoscope   | 19            | 2026-02-04  | Y      | 1           | 1039          | 1069          
joannacollins | Jo Collins       | Sanger      | 7             | 2026-01-16  | Y      | 1           | 1030          | 1060          
DomAbsolon    | Dom Absolon      | Sanger      | 8             | 2025-11-04  | Y      | 1           | 1029          | 1059          
MartinPippel  | Martin Pippel    | SciLifeLab  | 4             | 2026-01-30  | Y      | 1           | 1026          | 1056          
bistace       | Benjamin Istace  | Genoscope   | 13            | 2026-02-03  | Y      | 2           | 1045          | 1055          
gbdias        | Guilherme Dias   | SciLifeLab  | 6             | 2026-01-23  | Y      | 1           | 1024          | 1054          
additive3     | Jo Wood          | Sanger      | 8             | 2025-10-17  | Y      | 1           | 1029          | 1054          
auryjm        | Jean-Marc Aury   | Genoscope   | 14            | 2026-01-27  | Y      | 2           | 1043          | 1053          
tommathers    | Tom Mathers      | Sanger      | 7             | 2025-10-16  | Y      | 2           | 1030          | 1040          
SarahPelan    | Sarah Pelan      | Sanger      | 7             | 2025-12-19  | Y      | 2           | 1030          | 1040          
tbrown91      | Tom Brown        | IZW         | 12            | 2026-01-22  | Y      | 0           | 995           | 1040          
diegomics     | Diego De Panis   | IZW         | 11            | 2025-09-22  | Y      | 0           | 993           | 1038          
msozzoni      | Marcella Sozzoni | UNIFI       | 1             | 2026-02-05  | Y      | 2           | 1007          | 1017          

Selected reviewer: Lola Demirdjian (ldemirdj)
The decision was based on:
- different institution ('Genoscope')
- active ('Y')
- working on 1 PR(s) currently
- highest adjusted calling score in this particular selection (1072)
  (Note: Adjusted score already considering -20 points due to 1 ongoing PR(s))

[erga-ear-bot]

Hi @ldemirdj, do you agree to review this assembly?
Please reply to this message only with Yes or No by 13-Feb-2026 at 22:25 CET

[tbrown91]

Hey @jesgomez I had a look through while we wait for a reviewer. Overall, it's looking very clean. I moved a couple of unlocs around - one in scaffold 1 and one I moved into the unscaffolded pieces as it seems to have signal with multiple scaffolds. Hopefully you can pick them up from the savestate edits
iqPlaAffi.diploid_mq0.extensions.HR.pretext.savestate_1_tom.gz

[jesgomez]

thanks @tbrown91! I took a look at your savestate and I totally agree with edit 1. As for edit 2, it is true that H1_SUPER_9_unloc1 seems to correspond to telomeric sequence and that then it has contacts to many other places, but contacts seem to be stronger with SUPER_9. However, it is not so clear to me, so placing it in the chaff as you suggest, may seem the right thing to do.

Thanks again! Let's hope we get a reviewer soon and can finish this genome before the deadline ;)

[ldemirdj]

yes

[erga-ear-bot]

Thanks for agreeing!
I appointed you as the EAR reviewer.
I will track this as one of your Working PRs until you finish this review.
Please check the Wiki if you need to refresh something. (and remember that you must download the EAR PDF to be able to click on the link to the contact map file!)
Contact the PR assignee for any issues.

[ldemirdj]

Hi @jesgomez and @tbrown91, I have reviewed the EAR and the map. The assembly looks very well done. I agree with the modifications previously noted in the messages. Thank you both!

[jesgomez]

Great! I'll go ahead and produce and updated pdf. Thank you!!