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fPomQug EAR#293

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phuongdoand wants to merge 2 commits intoERGA-consortium:mainfrom
phuongdoand:phuongdoand-fPomQug-EAR
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fPomQug EAR#293
phuongdoand wants to merge 2 commits intoERGA-consortium:mainfrom
phuongdoand:phuongdoand-fPomQug-EAR

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@phuongdoand
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@phuongdoand phuongdoand commented Nov 27, 2025

Assembly review request

  • ToLID: fPomQug
  • Species: Pomatoschistus quagga
  • Project: ERGA-BGE
  • Affiliation: Genoscope

@erga-ear-bot
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erga-ear-bot bot commented Nov 27, 2025

Hi @phuongdoand, thanks for sending the EAR of Pomatoschistus quagga.
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 Nov 27, 2025

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

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erga-ear-bot bot commented Dec 4, 2025

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

@additive3
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additive3 commented Dec 4, 2025 via email

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erga-ear-bot bot commented Dec 4, 2025 

*****
EAR Reviewer Selection Process
Date: 2025-12-04 09:33

All Eligible Candidates:

Github ID     | Full Name             | Institution | Total Reviews | Last Review | Active | Working PRs | Calling Score | Adjusted Score
-----------------------------------------------------------------------------------------------------------------------------------------
talioto       | Tyler Alioto          | CNAG        | 8             | 2025-10-21  | Y      | 1           | 1029          | 1059          
gitcruz       | Fernando Cruz         | CNAG        | 13            | 2025-11-17  | Y      | 1           | 1025          | 1055          
MartinPippel  | Martin Pippel         | SciLifeLab  | 2             | 2025-10-06  | Y      | 1           | 1023          | 1053          
gbdias        | Guilherme Dias        | SciLifeLab  | 4             | 2025-11-19  | Y      | 1           | 1021          | 1051          
SarahPelan    | Sarah Pelan           | Sanger      | 6             | 2025-09-16  | Y      | 1           | 1019          | 1049          
joannacollins | Jo Collins            | Sanger      | 6             | 2025-10-10  | Y      | 1           | 1019          | 1049          
tommathers    | Tom Mathers           | Sanger      | 7             | 2025-10-16  | Y      | 1           | 1018          | 1048          
DomAbsolon    | Dom Absolon           | Sanger      | 8             | 2025-11-04  | Y      | 1           | 1017          | 1047          
additive3     | Jo Wood               | Sanger      | 8             | 2025-10-17  | Y      | 1           | 1017          | 1042          
diegomics     | Diego De Panis        | IZW         | 11            | 2025-09-22  | Y      | 0           | 992           | 1037          
jesgomez      | Jessica Gomez Garrido | CNAG        | 12            | 2025-11-26  | Y      | 2           | 1026          | 1036          
tbrown91      | Tom Brown             | IZW         | 11            | 2025-07-29  | Y      | 1           | 995           | 1020          

Selected reviewer: Tyler Alioto (talioto)
The decision was based on:
- different institution ('CNAG')
- active ('Y')
- working on 1 PR(s) currently
- highest adjusted calling score in this particular selection (1059)
  (Note: Adjusted score already considering -20 points due to 1 ongoing PR(s))

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erga-ear-bot bot commented Dec 4, 2025

Hi @talioto, do you agree to review this assembly?
Please reply to this message only with Yes or No by 10-Dec-2025 at 14:33 CET

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talioto commented Dec 5, 2025 via email

@erga-ear-bot erga-ear-bot bot requested a review from talioto December 5, 2025 13:20
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erga-ear-bot bot commented Dec 5, 2025

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.

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erga-ear-bot bot commented Dec 12, 2025

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

@talioto
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talioto commented Dec 18, 2025

I thought I'd replied here. Guess not. Um, first comment is that the density of contacts is so low, I can't really evaluate how well the scaffolding is done. There may be a lot of false joins, but it's really hard to tell. There should be like twice as many chromosomes as you have superscaffolds. you only have ten, whereas there should be ~22-24.

I think fPomQug_3 end is inverted. Some haplotigs here and there.

@erga-ear-bot erga-ear-bot bot added the DELAYED label Dec 25, 2025
@additive3
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additive3 commented Jan 11, 2026

@phuongdoand
I'd agree with @talioto assessment regrding the interpretability of the contact map. There looks to be some structural errors and many of the larger unassigned scaffolds look placeable.
Would you be able to provide the normal resolutiuon contact map so I can confirm this a bit better?

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additive3 commented Jan 22, 2026

@phuongdoand an update in providing the normal resolution pretext contact map?

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talioto commented Feb 2, 2026

@phuongdoand , please move on this. End of project approaching

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phuongdoand commented Feb 2, 2026

@additive3 @talioto Sorry for the late response, here is the link to the normal resolution contact map of fPomQug

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additive3 commented Feb 2, 2026

Hi @phuongdoand @talioto

Thanks for providing the normal resolution map. Greatly helps with sorting join errors. This is a tricky genome! and quite unusual (at least from what sequenced/karyotyped) in the low number of chromosomes it has.
Appears to be 9 chromosomes (2n=18), I think too there is quite abit of divergence between haplotypes hence low completeness for the primary assembly.
I've attached a savestate (txt for attach purposes) with changes made.
fPomQug_nm.pretext.map.savestate_jmdw.txt

@phuongdoand
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phuongdoand commented Feb 4, 2026

@additive3
Thank you for the modification. I just took a look at the savestate and there is a point that I think need clarification

  • scaffold 44, 56, 51 is painted as chrome 3 but I think they should belong to chrom 2?

@additive3
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additive3 commented Feb 4, 2026

Hi @phuongdoand

Thanks for your query. No those sequences are correctly attributed to chromosome scaffold 3.
Much of the interaction you are seeing to chromosome scaffold 2 are to the repeat blocks, there is high intereaction to the start of 3 for those small contigs that guides my placement.

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erga-ear-bot bot commented Feb 5, 2026

Attention @talioto, the EAR PDF was updated.

@additive3
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additive3 commented Feb 5, 2026

Thanks @phuongdoand

Happy to sign off on this assembly once @talioto checks

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