qqAmiAura12 EAR

[talioto]

Assembly review request

• ToLID: qqAmiAura12
• Species: Amilenus aurantiacus
• Project: ERGA-BGE
• Affiliation: CNAG

[erga-ear-bot]

Hi @talioto, thanks for sending the EAR of Amilenus aurantiacus.
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 From: "erga-ear-bot[bot]" ***@***.***> Reply to: ERGA-consortium/EARs ***@***.***> Date: Friday 21 February 2025 at 14:46 To: ERGA-consortium/EARs ***@***.***> Cc: Jo Wood ***@***.***>, Mention ***@***.***> Subject: Re: [ERGA-consortium/EARs] qqAmiAura12 EAR (PR #162) [EXT] Hi @additive3 [github.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_additive3&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=TUaG6OqjPfI1I0rzJIbKqE8Tjv85ynPYIkNbCjRS2SI&m=PrWstvzL1p3IhOihBNLvYKCSfCub4AchPXWyYRBhPFyYkNQcxOrwM4nU9CI1pUt-&s=M3UoFO2iaNFsErV91a63EmGWkT79C9ul2MrPxxhCULI&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=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=TUaG6OqjPfI1I0rzJIbKqE8Tjv85ynPYIkNbCjRS2SI&m=PrWstvzL1p3IhOihBNLvYKCSfCub4AchPXWyYRBhPFyYkNQcxOrwM4nU9CI1pUt-&s=MoAnRmqcn3_3QxHtPiVl00UkgS5ESVkhrDA3VfB8BJ8&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_162-23issuecomment-2D2674742339&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=TUaG6OqjPfI1I0rzJIbKqE8Tjv85ynPYIkNbCjRS2SI&m=PrWstvzL1p3IhOihBNLvYKCSfCub4AchPXWyYRBhPFyYkNQcxOrwM4nU9CI1pUt-&s=QvDrpq83F_WpqOxnbTXqSOymGV5ZxDRgZXUCC6WG_LA&e=>, or unsubscribe [github.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AEFJV4L22O7HFRKLEUK3CRT2Q433PAVCNFSM6AAAAABXTMZLQ6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMNZUG42DEMZTHE&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=TUaG6OqjPfI1I0rzJIbKqE8Tjv85ynPYIkNbCjRS2SI&m=PrWstvzL1p3IhOihBNLvYKCSfCub4AchPXWyYRBhPFyYkNQcxOrwM4nU9CI1pUt-&s=POScQ0A9pkTBp2GZNZ7dVCumldLHXrnT57PwhAmRWHg&e=>. You are receiving this because you were mentioned.Message ID: ***@***.***> [Image removed by sender. erga-ear-bot[bot]]erga-ear-bot[bot] left a comment (ERGA-consortium/EARs#162) [github.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_ERGA-2Dconsortium_EARs_pull_162-23issuecomment-2D2674742339&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=TUaG6OqjPfI1I0rzJIbKqE8Tjv85ynPYIkNbCjRS2SI&m=PrWstvzL1p3IhOihBNLvYKCSfCub4AchPXWyYRBhPFyYkNQcxOrwM4nU9CI1pUt-&s=QvDrpq83F_WpqOxnbTXqSOymGV5ZxDRgZXUCC6WG_LA&e=> Hi @additive3 [github.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_additive3&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=TUaG6OqjPfI1I0rzJIbKqE8Tjv85ynPYIkNbCjRS2SI&m=PrWstvzL1p3IhOihBNLvYKCSfCub4AchPXWyYRBhPFyYkNQcxOrwM4nU9CI1pUt-&s=M3UoFO2iaNFsErV91a63EmGWkT79C9ul2MrPxxhCULI&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=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=TUaG6OqjPfI1I0rzJIbKqE8Tjv85ynPYIkNbCjRS2SI&m=PrWstvzL1p3IhOihBNLvYKCSfCub4AchPXWyYRBhPFyYkNQcxOrwM4nU9CI1pUt-&s=MoAnRmqcn3_3QxHtPiVl00UkgS5ESVkhrDA3VfB8BJ8&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_162-23issuecomment-2D2674742339&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=TUaG6OqjPfI1I0rzJIbKqE8Tjv85ynPYIkNbCjRS2SI&m=PrWstvzL1p3IhOihBNLvYKCSfCub4AchPXWyYRBhPFyYkNQcxOrwM4nU9CI1pUt-&s=QvDrpq83F_WpqOxnbTXqSOymGV5ZxDRgZXUCC6WG_LA&e=>, or unsubscribe [github.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AEFJV4L22O7HFRKLEUK3CRT2Q433PAVCNFSM6AAAAABXTMZLQ6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMNZUG42DEMZTHE&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=TUaG6OqjPfI1I0rzJIbKqE8Tjv85ynPYIkNbCjRS2SI&m=PrWstvzL1p3IhOihBNLvYKCSfCub4AchPXWyYRBhPFyYkNQcxOrwM4nU9CI1pUt-&s=POScQ0A9pkTBp2GZNZ7dVCumldLHXrnT57PwhAmRWHg&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: 2025-02-21 14:53

All Eligible Candidates:

Github ID | Full Name      | Institution | Total Reviews | Last Review | Active | Busy | Calling Score | Adjusted Score
-----------------------------------------------------------------------------------------------------------------------
EmilieTeo | Emilie Teodori | Genoscope   | 3             | 2025-02-20  | Y      | N    | 1018          | 1068          
andar27   | Adama Ndar     | Genoscope   | 3             | 2025-02-21  | Y      | N    | 1018          | 1068          
diegomics | Diego De Panis | IZW         | 8             | 2024-10-22  | Y      | N    | 991           | 986           

Selected reviewer: Emilie Teodori (EmilieTeo)
The decision was based on:
- different institution ('Genoscope')
- active ('Y')
- not busy ('N')
- oldest review and fewest reviews among the finalists (1068)

[erga-ear-bot]

Hi @EmilieTeo, do you agree to review this assembly?
Please reply to this message only with Yes or No by 27-Feb-2025 at 19:53 CET

[EmilieTeo]

Yes

[erga-ear-bot]

Thanks for agreeing!
I appointed you as the EAR reviewer.
I will keep your status as Busy 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 @talioto

Here are my few suggestions :

• Invert SUPER_1 49.29-50.52Mb
• Invert SUPER_4 36.50-37.37Mb
• Move scaffold_2 to SUPER_2 as unloc

It's difficult to see any more changes that could be necessary since there isn't a lot of contacts outside of the main scaffolds, especially for the shrapnels

Best,
Emilie

[talioto]

Invert SUPER_1 49.29-50.52Mb Done.
Invert SUPER_4 36.50-37.37Mb Actually, I needed to invert 37-42
Move scaffold_2 to SUPER_2 as unloc

Additionally, based on hap1 pretext, looking at mq0, mq20 and mq40, I localized the three unloc scaffolds of SUPER_10.
New savestate here: https://ccnag-my.sharepoint.com/:u:/g/personal/tyler_alioto_cnag_eu/ETAyHoxunl5MrMuYDCkiig8B77-8pC3Ni3sy7Wdsiok72g?e=T2fMdv

These spiders we're working on are highly repetitive. The unplaced sqequence corresponds to repetitive sequence that is hard to uniquely place.

[EmilieTeo]

Yes, you're right I wrote the coordinates wrong, it was the region 37-42 in SUPER_4 that needed to be inverted
I opened your savestate and it looks good to me. I agree with the changes in SUPER_10 as well

Best,
Emilie

[additive3]

@talioto
I don't really have much to add. Was going to suggest that SUPER_10 pieces could be merged into single chromosome scaffold.
If you have mq 0 map. It would be really helpful from QC perspective to review this..for any genome. Filtering out repeats makes it hard to guage scaffold integrity and unloc sequences.

Best,
Jo

[talioto]

I did refer to the mq0 map of the yahs scaffolds, but I find it difficult to curate both at the same time. It's here if you want to try to make sense of it. https://ccnag-my.sharepoint.com/:u:/r/personal/tyler_alioto_cnag_eu/Documents/AAT/Curation/ERGA_Genomes/qqAmiAura12/qqAmiAura_hifiasm.prim.mq0.extensions.pretext?csf=1&web=1&e=4kKcbW
Since for the EAR we share the curated, re-mapped contact map, it's hard to go back and forth. From now on, we will try to produce mq0 and mq40 maps for everything we look at. BTW, is there an intermediate MQ that works better? MQ1, MQ5, MQ10???

[additive3]

@talioto there isn't a significant difference with any mq score >0

[additive3]

@talioto I do not have access to the file you just posted

[talioto]

sorry. here: https://ccnag-my.sharepoint.com/:u:/g/personal/tyler_alioto_cnag_eu/EdPhnFt5eHxEtlVhc0LGfP8BAJI2wio2AGb_xVryTuMahA?e=zbDNpQ
Again, it's on the yahs scaffolds and not the curated assembly.

[talioto]

Are you waiting for me? I suppose I will generate a new EAR and share both the mq0 and mq40 maps...