ERGA Assembly Report: Clavelina lepadiformis - kaClaLepa1

[mahesh-panchal]

Assembly review request

• ToLID: kaClaLepa1
• Species: Clavelina lepadiformis
• Project: ERGA-BGE
• Affiliation: SciLifeLab

[erga-ear-bot]

Hi @mahesh-panchal, thanks for sending the EAR of Clavelina lepadiformis.
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 09:05

All Eligible Candidates:

Github ID     | Full Name             | Institution | Total Reviews | Last Review | Active | Working PRs | Calling Score | Adjusted Score
-----------------------------------------------------------------------------------------------------------------------------------------
bistace       | Benjamin Istace       | Genoscope   | 13            | 2026-02-03  | Y      | 1           | 1045          | 1075          
ldemirdj      | Lola Demirdjian       | Genoscope   | 15            | 2026-02-04  | Y      | 1           | 1042          | 1072          
CaroB-M       | Caroline Menguy       | Genoscope   | 19            | 2026-02-04  | Y      | 1           | 1039          | 1069          
joannacollins | Jo Collins            | Sanger      | 7             | 2026-01-16  | Y      | 1           | 1029          | 1059          
DomAbsolon    | Dom Absolon           | Sanger      | 8             | 2025-11-04  | Y      | 1           | 1028          | 1058          
jesgomez      | Jessica Gomez Garrido | CNAG        | 16            | 2026-02-02  | Y      | 1           | 1027          | 1057          
additive3     | Jo Wood               | Sanger      | 8             | 2025-10-17  | Y      | 1           | 1028          | 1053          
auryjm        | Jean-Marc Aury        | Genoscope   | 14            | 2026-01-27  | Y      | 2           | 1043          | 1053          
EmilieTeo     | Emilie Teodori        | Genoscope   | 16            | 2026-02-02  | Y      | 2           | 1041          | 1051          
talioto       | Tyler Alioto          | CNAG        | 9             | 2026-01-09  | Y      | 2           | 1033          | 1043          
tbrown91      | Tom Brown             | IZW         | 12            | 2026-01-22  | Y      | 0           | 995           | 1040          
gitcruz       | Fernando Cruz         | CNAG        | 14            | 2026-01-14  | Y      | 2           | 1030          | 1040          
tommathers    | Tom Mathers           | Sanger      | 7             | 2025-10-16  | Y      | 2           | 1029          | 1039          
SarahPelan    | Sarah Pelan           | Sanger      | 7             | 2025-12-19  | Y      | 2           | 1029          | 1039          
diegomics     | Diego De Panis        | IZW         | 11            | 2025-09-22  | Y      | 0           | 993           | 1038          
msozzoni      | Marcella Sozzoni      | UNIFI       | 1             | 2026-02-05  | Y      | 2           | 1006          | 1016          

Selected reviewer: Benjamin Istace (bistace)
The decision was based on:
- different institution ('Genoscope')
- active ('Y')
- working on 1 PR(s) currently
- highest adjusted calling score in this particular selection (1075)
  (Note: Adjusted score already considering -20 points due to 1 ongoing PR(s))

[erga-ear-bot]

Hi @bistace, do you agree to review this assembly?
Please reply to this message only with Yes or No by 13-Feb-2026 at 14:05 CET

[tbrown91]

Hey @mahesh-panchal

I had a look through while we're waiting for a reviewer. I don't think this will need too much work. I looked at the combined map - which was pretty clean

I'm wondering if the final ~700kb of hap1_P_1 is supposed to be an unloc

I'm not sure about chromosome 6 - see what you think of my suggested rearrangements.

I flipped chromosome 8 in hap2 for consistency

kaClaLepa1_hr_sanger-hic_hap1-hap2.pretext.savestate_1_tom.gz

[bistace]

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.

[bistace]

Hi @mahesh-panchal @tbrown91! I agree with Tom so I made my modifications based on his savestate. Here are some things that I could see (I limited myself since the HiC comes from two different individuals):

• hap2_8: flip from 8.6Mb to 8.7Mb
• hap2_9: flip from 1.0Mb to 1.7Mb and then from 1.8Mb to 1.9Mb. That makes hap1 and hap2 agree and the signal looks better too

Here is my savestate.

[mahesh-panchal]

I need to investigate. Something is off. My input map didn't have that end square on hap1, and I have no idea why hap2 chromosome 8 is flipped.