fPomQug EAR

[phuongdoand]

Assembly review request

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

[erga-ear-bot]

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.

[erga-ear-bot]

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

[erga-ear-bot]

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

[additive3]

OK From: "erga-ear-bot[bot]" ***@***.***> Reply to: ERGA-consortium/EARs ***@***.***> Date: Thursday, 27 November 2025 at 09:01 To: ERGA-consortium/EARs ***@***.***> Cc: Jo Wood ***@***.***>, Mention ***@***.***> Subject: Re: [ERGA-consortium/EARs] fPomQug EAR (PR #293) [EXT] erga-ear-bot[bot] left a comment (ERGA-consortium/EARs#293) [github. com] Hi @additive3 [github. com], do you agree to supervise [github. com] this assembly? Please reply to this message only with OK to give acknowledge. — Reply to this email [Image removed by sender.]erga-ear-bot[bot] left a comment (ERGA-consortium/EARs#293) [github.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_ERGA-2Dconsortium_EARs_pull_293-23issuecomment-2D3584818493&d=DwMCaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=TUaG6OqjPfI1I0rzJIbKqE8Tjv85ynPYIkNbCjRS2SI&m=JA0oy_xe9exzZTsv-585BmvwDGoupJT6G7HhA1f0kHDh394TFYPjdDEA0PB4RpPw&s=PL_QtMlqEqLPILDZzVWuvZA-0dei0PN784nNmKnpCfY&e=> Hi @additive3 [github.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_additive3&d=DwMCaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=TUaG6OqjPfI1I0rzJIbKqE8Tjv85ynPYIkNbCjRS2SI&m=JA0oy_xe9exzZTsv-585BmvwDGoupJT6G7HhA1f0kHDh394TFYPjdDEA0PB4RpPw&s=lSweZYwSmCzLvqfrzBuw8yPBsT7SzTgQFqmWe8EjzoE&e=>, do you agree to supervise [github.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_ERGA-2Dconsortium_EARs_wiki_Assignees-2Dsection&d=DwMCaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=TUaG6OqjPfI1I0rzJIbKqE8Tjv85ynPYIkNbCjRS2SI&m=JA0oy_xe9exzZTsv-585BmvwDGoupJT6G7HhA1f0kHDh394TFYPjdDEA0PB4RpPw&s=sdX7tGcje6-vi9lutR5_LKWshoJCTrkx1hBYwbQjm3k&e=> this assembly? Please reply to this message only with OK to give acknowledge. — Reply to this email directly, view it on GitHub [github.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_ERGA-2Dconsortium_EARs_pull_293-23issuecomment-2D3584818493&d=DwMCaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=TUaG6OqjPfI1I0rzJIbKqE8Tjv85ynPYIkNbCjRS2SI&m=JA0oy_xe9exzZTsv-585BmvwDGoupJT6G7HhA1f0kHDh394TFYPjdDEA0PB4RpPw&s=PL_QtMlqEqLPILDZzVWuvZA-0dei0PN784nNmKnpCfY&e=>, or unsubscribe [github.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AEFJV4O2VAIPREA3URFMQTD3624VHAVCNFSM6AAAAACNLCQDWCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTKOBUHAYTQNBZGM&d=DwMCaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=TUaG6OqjPfI1I0rzJIbKqE8Tjv85ynPYIkNbCjRS2SI&m=JA0oy_xe9exzZTsv-585BmvwDGoupJT6G7HhA1f0kHDh394TFYPjdDEA0PB4RpPw&s=GVOtLIOMqEMAJ7ziphxCbVxvoaO6_Zj42IagN1RRvFY&e=>. You are receiving this because you were mentioned.Message ID: ***@***.***>

…

---------------------------------------------------------------------- The Wellcome Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA.

[erga-ear-bot]

*****
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))

[erga-ear-bot]

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

[talioto]

Yes

…

On Dec 4, 2025, at 10:33 AM, erga-ear-bot[bot] ***@***.***> wrote: erga-ear-bot[bot] left a comment (ERGA-consortium/EARs#293) <#293 (comment)> Hi @talioto <https://github.com/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 — Reply to this email directly, view it on GitHub <#293 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAI5CMLSRJYBQCMDPZJISK33775YDAVCNFSM6AAAAACNLCQDWCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTMMJRGEYDANJTGY>. 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.

[erga-ear-bot]

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

[talioto]

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.