Add qqGyaAnnu4 EAR

[tbrown91]

Assembly review request

• ToLID: qqGyaAnnu4
• Species: Gyas annulatus
• Project: ERGA-BGE
• Affiliation: IZW

[erga-ear-bot]

Hi @tbrown91, thanks for sending the EAR of Gyas annulatus.
I added the corresponding tag to the PR and will contact a supervisor and a reviewer ASAP.

[erga-ear-bot]

Hi @additive3, do you agree to supervise this assembly?
Please reply to this message only with OK to give acknowledge.

[additive3]

OK

[erga-ear-bot]

*****
EAR Reviewer Selection Process
Date: 2026-03-02 11:15

All Eligible Candidates:

Github ID     | Full Name             | Institution | Total Reviews | Last Review | Active | Working PRs | Calling Score | Adjusted Score
-----------------------------------------------------------------------------------------------------------------------------------------
talioto       | Tyler Alioto          | CNAG        | 10            | 2026-02-20  | Y      | 1           | 1043          | 1073          
additive3     | Jo Wood               | Sanger      | 10            | 2026-02-27  | Y      | 0           | 1028          | 1073          
EmilieTeo     | Emilie Teodori        | Genoscope   | 18            | 2026-02-17  | Y      | 1           | 1043          | 1073          
CaroB-M       | Caroline Menguy       | Genoscope   | 21            | 2026-02-24  | Y      | 1           | 1041          | 1071          
gitcruz       | Fernando Cruz         | CNAG        | 15            | 2026-02-13  | Y      | 1           | 1040          | 1070          
jesgomez      | Jessica Gomez Garrido | CNAG        | 18            | 2026-02-16  | Y      | 1           | 1036          | 1066          
DomAbsolon    | Dom Absolon           | Sanger      | 8             | 2025-11-04  | Y      | 1           | 1030          | 1060          
SarahPelan    | Sarah Pelan           | Sanger      | 8             | 2026-02-18  | Y      | 1           | 1030          | 1060          
tommathers    | Tom Mathers           | Sanger      | 8             | 2026-02-20  | Y      | 1           | 1030          | 1060          
joannacollins | Jo Collins            | Sanger      | 8             | 2026-02-24  | Y      | 1           | 1030          | 1060          
MartinPippel  | Martin Pippel         | SciLifeLab  | 5             | 2026-02-13  | Y      | 1           | 1027          | 1057          
bistace       | Benjamin Istace       | Genoscope   | 15            | 2026-02-20  | Y      | 2           | 1047          | 1057          
msozzoni      | Marcella Sozzoni      | UNIFI       | 3             | 2026-02-19  | Y      | 0           | 1006          | 1056          
gbdias        | Guilherme Dias        | SciLifeLab  | 7             | 2026-02-11  | Y      | 1           | 1025          | 1055          
auryjm        | Jean-Marc Aury        | Genoscope   | 16            | 2026-02-19  | Y      | 2           | 1045          | 1055          

Selected reviewer: Tyler Alioto (talioto)
The decision was based on:
- different institution ('CNAG')
- active ('Y')
- working on 1 PR(s) currently
- oldest review and fewest reviews among the finalists (1073)
  (Note: Adjusted score already considering -20 points due to 1 ongoing PR(s))

[erga-ear-bot]

Hi @talioto, do you agree to review this assembly?
Please reply to this message only with Yes or No by 06-Mar-2026 at 16:15 CET

[talioto]

Yes

[talioto]

@tbrown91 , can you fix the link to the contact map or just put it here in the chat?

Also, it doesn't look particularly contaminated but did you run FCS-GX or blobtools. There's no mention and the contact map is repeated instead of a bubble plot.

[erga-ear-bot]

Invalid confirmation!
Hi @talioto, do you agree to review this assembly?
Please reply to this message only with Yes or No by 09-Mar-2026 at 05:40 CET

[talioto]

Yes

…

On Mar 3, 2026, at 1:41 AM, erga-ear-bot[bot] ***@***.***> wrote: erga-ear-bot[bot] left a comment (ERGA-consortium/EARs#381) <#381 (comment)> Invalid confirmation! Hi @talioto <https://github.com/talioto>, do you agree to review this assembly? Please reply to this message only with Yes or No by 09-Mar-2026 at 05:40 CET — Reply to this email directly, view it on GitHub <#381 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAI5CMOXMREI6ZTUJPH7C7L4OYS2DAVCNFSM6AAAAACWDACFW2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTSOBXHA3TCNJYHE>. You are receiving this because you were mentioned.

[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.

[additive3]

@tbrown91 as @talioto has observed the embedded link for the qqGyaAnnu4 pretext file, isn't a link to file share.

[tbrown91]

Yes sorry both. I had to rush to produce something and then was away last week. I'll let you know once the link is ready

[erga-ear-bot]

Ping @additive3,
One week without any movements on this PR!

[erga-ear-bot]

Ping @additive3,
One week without any movements on this PR!

[talioto]

@tbrown91 , just post a link to the pretext here if you can. don't worry about updating the pdf.

[additive3]

Hi @tbrown91 @talioto

Gentle poke that the review contact map file is not available.

[erga-ear-bot]

Ping @additive3,
One week without any movements on this PR!

[tbrown91]

Hi both,

Here is the link for the maps: https://box.fu-berlin.de/s/bTXpFaCopaDbJNs

Apologies for the delay

[talioto]

Just to let you know that I'm now actively taking a look at this one. I will make some comments here and you can look at my savestate.

• SUPER_6 and SUPER_12 look like they can be joined. BUT, this would introduce a telomere in the middle. If we care about telomeric repeats in the center of supers, then we should probably revise SUPER_1, SUPER_2, SUPER_3 and SUPER_10 so that they don't join on telomeres (I've broken them up in my savestate). Can you confirm the telomeric repeat in the sequence and make sure it is repeated in tandem and not just enriched? TIDK uses a frequency in window approach, but on closer inspection, sometimes we can rule out some of the peaks.
• The repetitive contigs in SUPER_4 should probably be unloc. I don't see the evidence for their order and orientation. Maybe if you shared a map with a higher mq threshold it would help? Plenty of the shrapnel would appear to go here, too, but I'm worried that this is just an "attraction" point -- it could actually be placed in other chromosomes, too. I would break SUPER_4.
• weak support at SUPER_5:28.66. Not sure of orientation here. I changed it up but low confidence.

[additive3]

@tbrown91 @talioto

Nice to see a Harvestman genome!

Agree that SUPER_2, SUPER_3, SUPER_4 and SUPER_10 should be split.
I'd guess the repeat on SUPER_4 is terminal rDNA
SUPER_6/SUPER_12 think this is just a reflection of similar repeats giving elevated Hi-C signal and these should be separate.

SUPER_1.... hmmmmmmmm it is also possibly 2 joined because of all the repeat need to look more indepth at it.

Out of interest what was the identified telomere motif?

[talioto]

Seems like @additive3 and I are more or less in agreement. The ball's in your court, @tbrown91

[tbrown91]

Hey. Can you have a look at this?

qqGyaAnnu.tracks.pretext.savestate_1.gz

Telomere motif used was TTAGG

I'll be AFK again for a week or so now. I'll do what I can when I'm back

[talioto]

What is the MQ cutoff for this map? I feel like there is a lot of repeat attraction and it's hard to tell what really is contacting what. Also, maybe you could supply the assembly fasta file. I'd like to look a little closer at some sequence features.

[talioto]

@tbrown91 , can you please just finish this genome. If Jo approves, I'm fine.

[tbrown91]

@additive3 Chr1 is a mess, but I think the rest is looking in good shape.
If you can do anything, let me know. Otherwise hopefully we can Wrap it up