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Add icLarUrsu1#320
jesgomez wants to merge 3 commits intoERGA-consortium:mainfrom
jesgomez:icLarUrsu

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@jesgomez jesgomez commented Jan 12, 2026

Assembly review request

  • ToLID: icLarUrsu1
  • Species: Larinus ursus
  • Project: ERGA-BGE
  • Affiliation: CNAG

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erga-ear-bot bot commented Jan 12, 2026

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

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erga-ear-bot bot commented Jan 12, 2026

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

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tbrown91 commented Jan 12, 2026

ok

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erga-ear-bot bot commented Jan 12, 2026 

*****
EAR Reviewer Selection Process
Date: 2026-01-12 10:46

All Eligible Candidates:

Github ID     | Full Name       | Institution | Total Reviews | Last Review | Active | Working PRs | Calling Score | Adjusted Score
-----------------------------------------------------------------------------------------------------------------------------------
CaroB-M       | Caroline Menguy | Genoscope   | 16            | 2025-12-12  | Y      | 1           | 1038          | 1068          
joannacollins | Jo Collins      | Sanger      | 6             | 2025-10-10  | Y      | 1           | 1024          | 1054          
tommathers    | Tom Mathers     | Sanger      | 7             | 2025-10-16  | Y      | 1           | 1023          | 1053          
SarahPelan    | Sarah Pelan     | Sanger      | 7             | 2025-12-19  | Y      | 1           | 1023          | 1053          
bistace       | Benjamin Istace | Genoscope   | 11            | 2026-01-09  | Y      | 2           | 1043          | 1053          
DomAbsolon    | Dom Absolon     | Sanger      | 8             | 2025-11-04  | Y      | 1           | 1022          | 1052          
ldemirdj      | Lola Demirdjian | Genoscope   | 11            | 2025-10-14  | Y      | 2           | 1042          | 1052          
additive3     | Jo Wood         | Sanger      | 8             | 2025-10-17  | Y      | 1           | 1022          | 1047          
diegomics     | Diego De Panis  | IZW         | 11            | 2025-09-22  | Y      | 0           | 993           | 1038          
MartinPippel  | Martin Pippel   | SciLifeLab  | 2             | 2025-10-06  | Y      | 2           | 1025          | 1035          
gbdias        | Guilherme Dias  | SciLifeLab  | 4             | 2025-11-19  | Y      | 2           | 1023          | 1033          
auryjm        | Jean-Marc Aury  | Genoscope   | 12            | 2025-11-18  | Y      | 3           | 1041          | 1031          
tbrown91      | Tom Brown       | IZW         | 11            | 2025-07-29  | Y      | 1           | 996           | 1021          

Selected reviewer: Caroline Menguy (CaroB-M)
The decision was based on:
- different institution ('Genoscope')
- active ('Y')
- working on 1 PR(s) currently
- highest adjusted calling score in this particular selection (1068)
  (Note: Adjusted score already considering -20 points due to 1 ongoing PR(s))

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erga-ear-bot bot commented Jan 12, 2026

Hi @CaroB-M, do you agree to review this assembly?
Please reply to this message only with Yes or No by 16-Jan-2026 at 15:46 CET

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CaroB-M commented Jan 13, 2026

No

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erga-ear-bot bot commented Jan 13, 2026

@CaroB-M Ok thank you, I will look for the next reviewer on the list :)

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erga-ear-bot bot commented Jan 13, 2026 

*****
EAR Reviewer Selection Process
Date: 2026-01-13 15:05

All Eligible Candidates:

Github ID     | Full Name       | Institution | Total Reviews | Last Review | Active | Working PRs | Calling Score | Adjusted Score
-----------------------------------------------------------------------------------------------------------------------------------
tommathers    | Tom Mathers     | Sanger      | 7             | 2025-10-16  | Y      | 1           | 1023          | 1053          
SarahPelan    | Sarah Pelan     | Sanger      | 7             | 2025-12-19  | Y      | 1           | 1023          | 1053          
bistace       | Benjamin Istace | Genoscope   | 11            | 2026-01-09  | Y      | 2           | 1043          | 1053          
DomAbsolon    | Dom Absolon     | Sanger      | 8             | 2025-11-04  | Y      | 1           | 1022          | 1052          
ldemirdj      | Lola Demirdjian | Genoscope   | 11            | 2025-10-14  | Y      | 2           | 1042          | 1052          
CaroB-M       | Caroline Menguy | Genoscope   | 16            | 2025-12-12  | Y      | 2           | 1038          | 1048          
additive3     | Jo Wood         | Sanger      | 8             | 2025-10-17  | Y      | 1           | 1022          | 1047          
diegomics     | Diego De Panis  | IZW         | 11            | 2025-09-22  | Y      | 0           | 993           | 1038          
MartinPippel  | Martin Pippel   | SciLifeLab  | 2             | 2025-10-06  | Y      | 2           | 1025          | 1035          
joannacollins | Jo Collins      | Sanger      | 6             | 2025-10-10  | Y      | 2           | 1024          | 1034          
gbdias        | Guilherme Dias  | SciLifeLab  | 4             | 2025-11-19  | Y      | 2           | 1023          | 1033          
auryjm        | Jean-Marc Aury  | Genoscope   | 12            | 2025-11-18  | Y      | 3           | 1041          | 1031          
tbrown91      | Tom Brown       | IZW         | 11            | 2025-07-29  | Y      | 1           | 996           | 1021          

Selected reviewer: Tom Mathers (tommathers)
The decision was based on:
- different institution ('Sanger')
- active ('Y')
- working on 1 PR(s) currently
- oldest review and fewest reviews among the finalists (1053)
  (Note: Adjusted score already considering -20 points due to 1 ongoing PR(s))

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erga-ear-bot bot commented Jan 13, 2026

Hi @tommathers, do you agree to review this assembly?
Please reply to this message only with Yes or No by 19-Jan-2026 at 20:04 CET

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tommathers commented Jan 13, 2026 via email

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erga-ear-bot bot commented Jan 13, 2026

@tommathers Ok thank you, I will look for the next reviewer on the list :)

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erga-ear-bot bot commented Jan 13, 2026 

*****
EAR Reviewer Selection Process
Date: 2026-01-13 15:07

All Eligible Candidates:

Github ID     | Full Name       | Institution | Total Reviews | Last Review | Active | Working PRs | Calling Score | Adjusted Score
-----------------------------------------------------------------------------------------------------------------------------------
SarahPelan    | Sarah Pelan     | Sanger      | 7             | 2025-12-19  | Y      | 1           | 1023          | 1053          
bistace       | Benjamin Istace | Genoscope   | 11            | 2026-01-09  | Y      | 2           | 1043          | 1053          
DomAbsolon    | Dom Absolon     | Sanger      | 8             | 2025-11-04  | Y      | 1           | 1022          | 1052          
ldemirdj      | Lola Demirdjian | Genoscope   | 11            | 2025-10-14  | Y      | 2           | 1042          | 1052          
CaroB-M       | Caroline Menguy | Genoscope   | 16            | 2025-12-12  | Y      | 2           | 1038          | 1048          
additive3     | Jo Wood         | Sanger      | 8             | 2025-10-17  | Y      | 1           | 1022          | 1047          
diegomics     | Diego De Panis  | IZW         | 11            | 2025-09-22  | Y      | 0           | 993           | 1038          
MartinPippel  | Martin Pippel   | SciLifeLab  | 2             | 2025-10-06  | Y      | 2           | 1025          | 1035          
joannacollins | Jo Collins      | Sanger      | 6             | 2025-10-10  | Y      | 2           | 1024          | 1034          
gbdias        | Guilherme Dias  | SciLifeLab  | 4             | 2025-11-19  | Y      | 2           | 1023          | 1033          
tommathers    | Tom Mathers     | Sanger      | 7             | 2025-10-16  | Y      | 2           | 1023          | 1033          
auryjm        | Jean-Marc Aury  | Genoscope   | 12            | 2025-11-18  | Y      | 3           | 1041          | 1031          
tbrown91      | Tom Brown       | IZW         | 11            | 2025-07-29  | Y      | 1           | 996           | 1021          

Selected reviewer: Sarah Pelan (SarahPelan)
The decision was based on:
- different institution ('Sanger')
- active ('Y')
- working on 1 PR(s) currently
- oldest review and fewest reviews among the finalists (1053)
  (Note: Adjusted score already considering -20 points due to 1 ongoing PR(s))

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erga-ear-bot bot commented Jan 13, 2026

Hi @SarahPelan, do you agree to review this assembly?
Please reply to this message only with Yes or No by 19-Jan-2026 at 20:07 CET

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SarahPelan commented Jan 13, 2026

yes

@erga-ear-bot erga-ear-bot bot requested a review from SarahPelan January 13, 2026 15:12
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erga-ear-bot bot commented Jan 13, 2026

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.

SarahPelan
SarahPelan reviewed Jan 13, 2026
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Hi,
I've checked this one and here's what I think:

SUPER_1:
~43,880 and ~73,846 both look like retained haplotype

SUPER_1_unloc_1:
I think this looks like a chromosome rather than being part of SUPER_1, scaffold_58 can join this new chromosome, probably as an unloc piece

SUPER_2:
~80,964-81,231 needs to move to ~71,652

SUPER_3:
I think you can join the unloc piece in at ~63,358 but the piece from 6,367-end of unloc_1 looks like duplication so needs removing.

SUPER_4:
~20,709-21,565 looks like duplication of SUPER_18 ~21,940

SUPER_6:
I think that ~80,964 to the end needs to flip

SUPER_10:
I don’t think the sequence at the start 0-2,889 belongs here. I think it would be better in the shrapnel as it doesn’t convincingly seem to fit anywhere
~20,334-25,846 looks like retained haplotype
I think super_10_unloc 1 is retained haplotype
super_10_unloc_2 matches to a few other places so put in the shapnel

SUPER_13:
~35,211 joined on telomeres, break here and rejoin ends together

SUPER_15:
39,652-46,074 looks like this should flip but there are no gaps here? Can you check?

SUPER_20:
Can you check the telomere tag at ~4,923?
It looks like 0-4,923 might go in at ~16,374, multi mapping reads may help to place the first part of this piece

scaffold_20 can join into SUPER_20 at ~32,374
scaffold_41 looks like it belongs somewhere in SUPER_10
scaffold_68 looks like duplication
scaffold_63 can join to start of SUPER_6

It might help to include multi-mapping reads when you make your updated pretext if you haven’t already.

Thanks,
Sarah

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jesgomez commented Jan 15, 2026

uoo, that was really useful, thanks a lot Sarah!! I indded had several doubts with this one and you gave suggestions for most of those doubtful locations.

I implemented most of the changes you suggested,you can check by loading the new savestate I produced. You can find below some additional comments. BTW, this map is already including multimappings (it was obtained with mq0).

SUPER_1:
~43,880 and ~73,846 both look like retained haplotype --> which coordinates exactly? they look so small I'm not really sure here

SUPER_1_unloc_1:
I think this looks like a chromosome rather than being part of SUPER_1, scaffold_58 can join this new chromosome, probably as an unloc piece. --> thanks, this makes sense, I was unsure what to do here.
e
SUPER_2:
~80,964-81,231 needs to move to ~71,652 --> I agree, done

SUPER_3:
I think you can join the unloc piece in at ~63,358 but the piece from 6,367-end of unloc_1 looks like duplication so needs removing. --> I agree, done

SUPER_4:
~20,709-21,565 looks like duplication of SUPER_18 ~21,940 --> I agree, done

SUPER_6:
I think that ~80,964 to the end needs to flip --> I agree, done

SUPER_10:
I don’t think the sequence at the start 0-2,889 belongs here. I think it would be better in the shrapnel as it doesn’t convincingly seem to fit anywhere --> I agree, done
~20,334-25,846 looks like retained haplotype --> I agree, done
I think super_10_unloc 1 is retained haplotype --> I agree, done
super_10_unloc_2 matches to a few other places so put in the shapnel --> I agree, done

SUPER_13:
~35,211 joined on telomeres, break here and rejoin ends together --> it makes sense, I flipped this piece

SUPER_15:
39,652-46,074 looks like this should flip but there are no gaps here? Can you check? --> yes there are no gaps, but it looks much better this way, I broke it.

SUPER_20:
Can you check the telomere tag at ~4,923?
It looks like 0-4,923 might go in at ~16,374, multi mapping reads may help to place the first part of this piece --> I placed from ~1765 - ~4923 in 16374, despite of the telomeric peak, I agree it seems to fit thre. As for the begining, and given that this map is already mq0, I think it may go better into the shrapnel, what do you think? It's not very specific...

scaffold_20 can join into SUPER_20 at ~32,374 --> I agree, done
scaffold_41 looks like it belongs somewhere in SUPER_10 --> I agree, done
scaffold_68 looks like duplication --> I agree, done
scaffold_63 can join to start of SUPER_6 --> I agree, done

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jesgomez commented Jan 15, 2026

Direct link to the savestate: https://ccnag-my.sharepoint.com/:u:/g/personal/tyler_alioto_cnag_eu/IQAu0KoCfkAzT4etbBlssLQiATCAl8PJVAR9oRfecGzfjBc?e=tQFLIZ

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SarahPelan commented Jan 16, 2026

Hi again,

SUPER_1:
~43,880 and ~73,846 both look like retained haplotype --> which coordinates exactly? they look so small I'm not really sure here

43,880-44,308Kbp and 73,044-73,846. Off diagonal signals and coverage drop here

SUPER_13:
~35,211 joined on telomeres, break here and rejoin ends together --> it makes sense, I flipped this piece

I don’t think this flips, just break and join ends together in the same orientation.

SUPER_15:
39,652-46,074 looks like this should flip but there are no gaps here? Can you check? --> yes there are no gaps, but it looks much better this way, I broke it.

I wouldn’t remove the piece you have tagged as haplotig in your savestate, looks like just repetitive region and should be included

SUPER_20:
Can you check the telomere tag at ~4,923?
It looks like 0-4,923 might go in at ~16,374, multi mapping reads may help to place the first part of this piece --> I placed from ~1765 - ~4923 in 16374, despite of the telomeric peak, I agree it seems to fit thre. As for the begining, and given that this map is already mq0, I think it may go better into the shrapnel, what do you think? It's not very specific...

I agree, add super_20 0-1,658kbp to shrapnel

Thanks,
Sarah

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jesgomez commented Jan 19, 2026

ok, thank you Sarah. I applied the last changes you suggested, you can check them in savestate_3 if you wish. Now, if you all agree I'll produce an updated genome and submit the editted EAR soon.

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SarahPelan commented Jan 20, 2026

Can you send a link to your savestate_3 if you want me to look?
Thanks

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jesgomez commented Jan 20, 2026

https://ccnag-my.sharepoint.com/:f:/g/personal/tyler_alioto_cnag_eu/IgCyVMu6M6CVQoXDGL_MGSiVAQC114u7h5TdX5ZH_EfINuk?e=56V5P4

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SarahPelan commented Jan 20, 2026

That looks sensible thanks.
Just be aware that where you have moved parts of SUPER named things to shrapnel, you might have to rename them as if you're using our pipeline to generate the fasta, it won't like it as there will be duplicated names..
If you generate the new map, I'll check it one final time and then it should be good to go
Thanks

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erga-ear-bot bot commented Jan 27, 2026

Ping @tbrown91,
One week without any movements on this PR!

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erga-ear-bot bot commented Jan 30, 2026

Attention @tbrown91, the EAR PDF was updated.

@jesgomez
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jesgomez commented Feb 5, 2026

Hi @SarahPelan, I updated the pdf. Let me know if it looks good to you now. Thanks!

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SarahPelan commented Feb 5, 2026

Hi @jesgomez
Just to double check, is
reviewd_icLarUrsu1.1.primary.curated_mq0.extensions.HR.pretext
the pretext I should be looking at?

Thanks,
Sarah

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jesgomez commented Feb 5, 2026

yes

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SarahPelan commented Feb 5, 2026

Thanks,
I think that:
SUPER_5 from start to ~13,141 should flip, and then also from ~81,591 to the end should flip
SUPER_13 ~65,167-end needs to break and join to the left end of SUPER_13
SUPER_18 flip start- gap at 4,283 (if you wanted to, then 18_unloc_2 can go in the gap also)
SUPER_20, I would tag from ~40,755-end as unloc, or possibly move to join it in at ~29,289

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jesgomez commented Feb 6, 2026

Perfect, thank you. Here is the savestate with the changes: https://ccnag-my.sharepoint.com/:u:/g/personal/tyler_alioto_cnag_eu/IQBJ3ra3ldZeQ71ojVQQkp2IAe-zTXA8SS7T3-XTNmxeJyQ?e=WDihEE

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SarahPelan commented Feb 6, 2026

Hi again,
I can't get the savestate to load into my pretext..

@jesgomez
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jesgomez commented Feb 6, 2026

mm try now: https://ccnag-my.sharepoint.com/:u:/g/personal/tyler_alioto_cnag_eu/IQBJ3ra3ldZeQ71ojVQQkp2IAe-zTXA8SS7T3-XTNmxeJyQ?e=snrbL4

@SarahPelan
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SarahPelan commented Feb 6, 2026

No, still can't get it to work..

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jesgomez commented Feb 6, 2026

ok, try using the pretext and savestate in this new directory: https://ccnag-my.sharepoint.com/:f:/g/personal/tyler_alioto_cnag_eu/IgD-GDb23J1pTq1Db-pOR9P7AUTgpyoOtg0pnoIhaLq3Er8?e=Tv9HWW

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SarahPelan commented Feb 10, 2026

@jesgomez
Yes, that worked thank you.
Changes look good to me

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tbrown91 commented Feb 11, 2026

Thank you @SarahPelan

@jesgomez I guess you can go ahead with uploading the assembly with these changes if it helps things on your end. We'll just wait for the updated pdf

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jesgomez commented Feb 11, 2026

thank you both! I'll prepare the updated pdf and the ENA submission.

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erga-ear-bot bot commented Feb 13, 2026

Attention @tbrown91, the EAR PDF was updated.

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SarahPelan commented Feb 13, 2026

Hi @jesgomez
Sorry I missed something else :(

SUPER_12
~27,986-29,263 looks like a hap/false dup here

If you agree and are going to change the map anyway, I think that on reflection, the piece on SUPER_5 from ~12,450-13,141 would be better as an unloc if you agree.

This will definitely be it now, so if you agree and do change them then go ahead and prepare an updated pdf and I can get this one updated
Thanks for making all the changes!
Sarah

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