initial commit Scarites_abbreviatus - icScaAbbr5

[MartinPippel]

Assembly review request

• ToLID: icScaAbbr5
• Species: Scarites abbreviatus
• Project: ERGA-BGE
• Affiliation: SciLifeLab

[erga-ear-bot]

Hi @MartinPippel, thanks for sending the EAR of Scarites abbreviatus.
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.

[tbrown91]

ok

[erga-ear-bot]

*****
EAR Reviewer Selection Process
Date: 2026-01-19 09:51

All Eligible Candidates:

Github ID     | Full Name             | Institution | Total Reviews | Last Review | Active | Working PRs | Calling Score | Adjusted Score
-----------------------------------------------------------------------------------------------------------------------------------------
DomAbsolon    | Dom Absolon           | Sanger      | 8             | 2025-11-04  | Y      | 0           | 1022          | 1072          
bistace       | Benjamin Istace       | Genoscope   | 11            | 2026-01-09  | Y      | 2           | 1044          | 1054          
tommathers    | Tom Mathers           | Sanger      | 7             | 2025-10-16  | Y      | 1           | 1023          | 1053          
joannacollins | Jo Collins            | Sanger      | 7             | 2026-01-16  | Y      | 1           | 1023          | 1053          
ldemirdj      | Lola Demirdjian       | Genoscope   | 11            | 2025-10-14  | Y      | 2           | 1043          | 1053          
CaroB-M       | Caroline Menguy       | Genoscope   | 16            | 2025-12-12  | Y      | 2           | 1039          | 1049          
additive3     | Jo Wood               | Sanger      | 8             | 2025-10-17  | Y      | 1           | 1022          | 1047          
talioto       | Tyler Alioto          | CNAG        | 9             | 2026-01-09  | Y      | 2           | 1030          | 1040          
diegomics     | Diego De Panis        | IZW         | 11            | 2025-09-22  | Y      | 0           | 993           | 1038          
gitcruz       | Fernando Cruz         | CNAG        | 14            | 2026-01-14  | Y      | 2           | 1027          | 1037          
jesgomez      | Jessica Gomez Garrido | CNAG        | 14            | 2025-12-19  | Y      | 2           | 1026          | 1036          
SarahPelan    | Sarah Pelan           | Sanger      | 7             | 2025-12-19  | Y      | 2           | 1023          | 1033          
auryjm        | Jean-Marc Aury        | Genoscope   | 12            | 2025-11-18  | Y      | 3           | 1042          | 1032          
tbrown91      | Tom Brown             | IZW         | 11            | 2025-07-29  | Y      | 1           | 996           | 1021          

Selected reviewer: Dom Absolon (DomAbsolon)
The decision was based on:
- different institution ('Sanger')
- active ('Y')
- working on 0 PR(s) currently
- highest adjusted calling score in this particular selection (1072)

[erga-ear-bot]

Hi @DomAbsolon, do you agree to review this assembly?
Please reply to this message only with Yes or No by 23-Jan-2026 at 14:51 CET

[DomAbsolon]

Yes From: "erga-ear-bot[bot]" ***@***.***> Reply to: ERGA-consortium/EARs ***@***.***> Date: Monday, 19 January 2026 at 09:52 To: ERGA-consortium/EARs ***@***.***> Cc: Dominic Absolon ***@***.***>, Mention ***@***.***> Subject: Re: [ERGA-consortium/EARs] initial commit Scarites_abbreviatus - icScaAbbr5 (PR #325) [EXT] erga-ear-bot[bot] left a comment (ERGA-consortium/EARs#325) [github. com] Hi @DomAbsolon [github. com], do you agree to review this assembly? Please reply to this message only with Yes or No by 23-Jan-2026 at 14: 51 CET — Reply to this email [Image removed by sender.]erga-ear-bot[bot] left a comment (ERGA-consortium/EARs#325) [github.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_ERGA-2Dconsortium_EARs_pull_325-23issuecomment-2D3767422590&d=DwMCaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=HMo-nEncpJD-Huct-h6WEs_n6mFGlpSnfDTSEb1TwXE&m=iGxvMEL--J3r4uOT1O1ZXBfc42bMXrjU6XZmmat8kBSz4ARyICd50idKtFVKu_Bc&s=nLkxSwYiauKxIoehTmfwd0n9PXDtZJ6jxsOyLxYsTQw&e=> Hi @DomAbsolon [github.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_DomAbsolon&d=DwMCaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=HMo-nEncpJD-Huct-h6WEs_n6mFGlpSnfDTSEb1TwXE&m=iGxvMEL--J3r4uOT1O1ZXBfc42bMXrjU6XZmmat8kBSz4ARyICd50idKtFVKu_Bc&s=B4fl0p6EeTVPq2MTsvH_hvDFXqI-VGw1_FGH1KGTRis&e=>, do you agree to review this assembly? Please reply to this message only with Yes or No by 23-Jan-2026 at 14:51 CET — 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_325-23issuecomment-2D3767422590&d=DwMCaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=HMo-nEncpJD-Huct-h6WEs_n6mFGlpSnfDTSEb1TwXE&m=iGxvMEL--J3r4uOT1O1ZXBfc42bMXrjU6XZmmat8kBSz4ARyICd50idKtFVKu_Bc&s=nLkxSwYiauKxIoehTmfwd0n9PXDtZJ6jxsOyLxYsTQw&e=>, or unsubscribe [github.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_BCJBKICGNBLYM2T6MJVXWHT4HSSNJAVCNFSM6AAAAACSAJ3YEOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTONRXGQZDENJZGA&d=DwMCaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=HMo-nEncpJD-Huct-h6WEs_n6mFGlpSnfDTSEb1TwXE&m=iGxvMEL--J3r4uOT1O1ZXBfc42bMXrjU6XZmmat8kBSz4ARyICd50idKtFVKu_Bc&s=wf6IhhZBsnMc59R96GFdb6gim2H-KAEvZMvo6H21dT0&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]

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

[tbrown91]

@DomAbsolon are you able to look through this one?

[DomAbsolon]

Hi Martin, pretty tricky assembly to curate. There are two joins I'm almost certain on: h2_s15 + h2_s26 and h2_s25 + h2_s16

Note that you have the maps and file systems mixed up so the map in the hap1 date repo has headers "h2" whereas presumably that should be "h1".

The other thing that might help confirm arm interaction is making a map with filtered multi-mapping reads (-q 10). This can help reveal the long range interactions between arms in beetles

[tbrown91]

icScaAbbr.hap1.normal.pretext.savestate_1.gz
Hey @MartinPippel can you have a look at this? This is from the hap1 (h2?) map

The hap2 (h1) map is looking a lot better, but I'm not sure that the 26th scaffold should be its own chromosome

[MartinPippel]

Hej @DomAbsolon, hej @tbrown91,

thanks for the comments and sorry for the file naming issues. I recognised just at the very end of the curation that the X-chromosome was still located in haplotype 2 and I didn't want to rerun all steps again. Therefore I just renamed the files.
(I was expecting many suggestions anyway ;)

The phasing of the genome didn't really work well, therefore the hap 2 is much larger than hap 1. I will move the X to hap 1 and apply the two changes that you suggested in both haplotypes.
@tbrown91 I cannot open that save state file - or at least I do not see any changes. Do you have additional comments?

[tbrown91]

Strange. It's not working for me either. Are you able to make the map with mapq 10? Otherwise I will have a look through on Monday - I'm not sure how far we can push this one

[MartinPippel]

a map with -q10 is loosing almost all signal in those repetitive regions. -q1 is keeping some signal - though not really revealing any more insights. I think we will never get the hap2 (currently named hap1) right. Though I think hap1 (currently named hap2) should be doable.
If you think we cannot finish this by the end of the deadline then I am quite pessimistic about my two other assemblies.

[DomAbsolon]

Hi Martin, is the -q10 map available anywhere ?

[MartinPippel]

I uploaded the q1 and q10 maps: icScaAbbr5