qqLeiRupe1 EAR

[gitcruz]

Assembly review request

• ToLID: qqLeiRupe1
• Species: Leiobunum rupestre
• Project: ERGA-BGE
• Affiliation: CNAG

[erga-ear-bot]

Hi @gitcruz, thanks for sending the EAR of Leiobunum rupestre.
I added the corresponding tag to the PR and will contact a supervisor and a reviewer ASAP.

[erga-ear-bot]

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

[diegomics]

ok

[erga-ear-bot]

*****
EAR Reviewer Selection Process
Date: 2026-02-10 13:03

All Eligible Candidates:

Github ID     | Full Name        | Institution | Total Reviews | Last Review | Active | Working PRs | Calling Score | Adjusted Score
------------------------------------------------------------------------------------------------------------------------------------
EmilieTeo     | Emilie Teodori   | Genoscope   | 17            | 2026-02-09  | Y      | 0           | 1040          | 1090          
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          
ldemirdj      | Lola Demirdjian  | Genoscope   | 15            | 2026-02-04  | Y      | 2           | 1042          | 1052          
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: Emilie Teodori (EmilieTeo)
The decision was based on:
- different institution ('Genoscope')
- active ('Y')
- working on 0 PR(s) currently
- highest adjusted calling score in this particular selection (1090)

[erga-ear-bot]

Hi @EmilieTeo, do you agree to review this assembly?
Please reply to this message only with Yes or No by 16-Feb-2026 at 18:03 CET

[EmilieTeo]

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.

[EmilieTeo]

Hi @gitcruz
This assembly looks really nice !
I agree with your observation regarding the inversion in SUPER_3
The only comment that I have is that the scaffolds H1_H1_scaffold_16 and H1_H1_scaffold_18 have a higher contact density with SUPER_11 than with the other scaffolds. I would tag them unloc

Best,
Emilie

[gitcruz]

Thanks for agreeing @EmilieTeo and @diegomics

As I wrote in the note please click on the link under the diploid map screenshot, this will direct you to shared folder. The open the normal resolution and open the savestate_1. I'd like youbto start form there and see if you can find anything else that we can fix.

Best,
Fernando

[gitcruz]

Thanks for the quieck review @EmilieTeo,

Yes. Although we originally considered them unplaced, these two scaffolds* are likely unlocs of HAP1. Let's see what Diego says before I paint everything again and produce the final fasta.

• H1_H1_scaffold_16 and H1_H1_scaffold_18

Cheers.

Hi @gitcruz This assembly looks really nice ! I agree with your observation regarding the inversion in SUPER_3 The only comment that I have is that the scaffolds H1_H1_scaffold_16 and H1_H1_scaffold_18 have a higher contact density with SUPER_11 than with the other scaffolds. I would tag them unloc

Best, Emilie

[diegomics]

I just did a quick pass. Looks really nice. Not much to add here to what Emilie commented. Some suspicious spots look fine after closer inspection, like H1_SUPER_10 gap @ ~52,897 and the start of H1_SUPER_10 (they look the same in H2...), this also happens in SUPER_3 at the end. All good from my side.

[gitcruz]

Thanks Diego,

So I will paint, produce savestate_2 and the final FASTAs to upload both haps to ENA. Could you merge this to the main branch?

Nando

[diegomics]

No. After @EmilieTeo approval, you are good to go for uploading the revised version to ENA. In the mean time you can regenerate the PDF. When the new PDF is pushed into the PR, I can proceed with the merging.

[gitcruz]

I don't think the stats will change dramatically (a few unlocs will increase tiny decimals in kmer completeness), what about placing savestate_final in the shared folder and keeping the same EAR? I will ping Emily when I am done with it Thanks, Nando

…

On Thu, 12 Feb 2026 at 12:39, Diego De Panis ***@***.***> wrote: *diegomics* left a comment (ERGA-consortium/EARs#348) <#348 (comment)> No. After @EmilieTeo <https://github.com/EmilieTeo> approval, you are good to go for uploading the revised version to ENA. In the mean time you can regenerate the PDF. When the new PDF is pushed into the PR, I can proceed with the merging. — Reply to this email directly, view it on GitHub <#348 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AB34KVICH52NJ3VVNGKEGJD4LRQ5VAVCNFSM6AAAAACUPP26ZGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTQOJQGQYTSMBWGU> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[gitcruz]

By the way @diegomics, WRT to your comments:

1. on H1_SUPER_10 gap @ ~52,897 it could be a FalseDuplicate present in both HAPs, so I could remove it after the gap in both Haplotyopes. What do you and @EmilieTeo think?

2. At the start of SUPER_10 in bith haps I think this is a subtelomeric repeat that was contigged in both haplotypes and is a real feature of this genome

[gitcruz]

Hi @EmilieTeo and @diegomics,

Please have a look at the latest savestate (qqLeiRupe1.diploid_mq0.extensions.pretext.savestate_2) removing False_Duplicates at HAP1+HAPSUPER_10 gap@ ~52,897

It's already painted and ready to go.

Thanks.
Fernando

By the way @diegomics, WRT to your comments:

1. on H1_SUPER_10 gap @ ~52,897 it could be a FalseDuplicate present in both HAPs, so I could remove it after the gap in both Haplotyopes. What do you and @EmilieTeo think?

2. At the start of SUPER_10 in bith haps I think this is a subtelomeric repeat that was contigged in both haplotypes and is a real feature of this genome