qdTypCoec2_EAR

[fcamara7]

Assembly review request

• ToLID: qdTypCoec2
• Species: Typhloglomeris coeca
• Project: ERGA-BGE
• Affiliation: CNAG

[erga-ear-bot]

Hi @fcamara7, thanks for sending the EAR of Typhloglomeris coeca.
I added the corresponding tag to the PR and will contact a supervisor and a reviewer ASAP.

[erga-ear-bot]

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

[diegomics]

ok

[erga-ear-bot]

*****
EAR Reviewer Selection Process
Date: 2026-01-30 12:59

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           | 1026          | 1056          
joannacollins | Jo Collins       | Sanger      | 7             | 2026-01-16  | Y      | 1           | 1026          | 1056          
DomAbsolon    | Dom Absolon      | Sanger      | 8             | 2025-11-04  | Y      | 1           | 1025          | 1055          
bistace       | Benjamin Istace  | Genoscope   | 12            | 2026-01-21  | Y      | 2           | 1045          | 1055          
gbdias        | Guilherme Dias   | SciLifeLab  | 6             | 2026-01-23  | Y      | 1           | 1024          | 1054          
auryjm        | Jean-Marc Aury   | Genoscope   | 14            | 2026-01-27  | Y      | 2           | 1042          | 1052          
ldemirdj      | Lola Demirdjian  | Genoscope   | 14            | 2026-01-29  | Y      | 2           | 1042          | 1052          
EmilieTeo     | Emilie Teodori   | Genoscope   | 15            | 2025-12-15  | Y      | 2           | 1041          | 1051          
additive3     | Jo Wood          | Sanger      | 8             | 2025-10-17  | Y      | 1           | 1025          | 1050          
CaroB-M       | Caroline Menguy  | Genoscope   | 17            | 2026-01-20  | Y      | 2           | 1040          | 1050          
msozzoni      | Marcella Sozzoni | UNIFI       | 0             | NA          | Y      | 3           | 1007          | 1047          
tbrown91      | Tom Brown        | IZW         | 12            | 2026-01-22  | Y      | 0           | 995           | 1040          
diegomics     | Diego De Panis   | IZW         | 11            | 2025-09-22  | Y      | 0           | 993           | 1038          
MartinPippel  | Martin Pippel    | SciLifeLab  | 3             | 2026-01-20  | Y      | 2           | 1027          | 1037          
SarahPelan    | Sarah Pelan      | Sanger      | 7             | 2025-12-19  | Y      | 2           | 1026          | 1036          

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 (1056)
  (Note: Adjusted score already considering -20 points due to 1 ongoing PR(s))

[erga-ear-bot]

Hi @tommathers, do you agree to review this assembly?
Please reply to this message only with Yes or No by 05-Feb-2026 at 17:59 CET

[tommathers]

yes Dr. Thomas Mathers Senior Computer Biologist Genome Reference Informatics Team Tree of Life Wellcome Sanger Institute Hinxton Cambridge CB10 1SA Twitter: @Thomas_Mathers [twitter.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__twitter.com_Thomas-5FMathers-3Flang-3Den-2Dgb&d=DwMGaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=MigC00eCez0AYiD8Bi3uR5vUblihAN7OJ3KK8sbnotw&m=tJRHixSYq-VP6FIxTiP35xdkMZl3FaXQVx1qay3XZ-7I4UkhUxDC7h1P98bVhcBb&s=hffLCC65eIfPsnmm3hnO-CV4DYCZYG2ebSippldU3zw&e=> Publications: Google Scholar [scholar.google.co.uk]<https://urldefense.proofpoint.com/v2/url?u=https-3A__scholar.google.co.uk_citations-3Fhl-3Den-26user-3D5XjBm94AAAAJ-26view-5Fop-3Dlist-5Fworks-26sortby-3Dpubdate&d=DwMFAg&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=MigC00eCez0AYiD8Bi3uR5vUblihAN7OJ3KK8sbnotw&m=KIKynKbLKfS4YVQYVctJHL39ls39CbRogxK7G0OumbwWdwS4Qdlkrg9NnRJHPJGs&s=T2pa4qY1i623xxULQ3x4gTTj4JvNcKbwYHoNm5knTFc&e=> From: "erga-ear-bot[bot]" ***@***.***> Reply to: ERGA-consortium/EARs ***@***.***> Date: Friday, 30 January 2026 at 12:59 To: ERGA-consortium/EARs ***@***.***> Cc: Thomas Mathers ***@***.***>, Mention ***@***.***> Subject: Re: [ERGA-consortium/EARs] qdTypCoec2_EAR (PR #343) [EXT] erga-ear-bot[bot] left a comment (ERGA-consortium/EARs#343) [github. com] Hi @tommathers [github. com], do you agree to review this assembly? Please reply to this message only with Yes or No by 05-Feb-2026 at 17: 59 CET — Reply to this email [Image removed by sender.]erga-ear-bot[bot] left a comment (ERGA-consortium/EARs#343) [github.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_ERGA-2Dconsortium_EARs_pull_343-23issuecomment-2D3823633007&d=DwMCaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=MigC00eCez0AYiD8Bi3uR5vUblihAN7OJ3KK8sbnotw&m=w_H3IPxeL55D3gCZzVCMORvLhjZPTTC7XfoC8-QykpUo-qFf6l8FY48mOXuB8unS&s=JNPs_LpDKLPAERxve19dL2OnEPPdyJPj9ZKnS1cl0Hk&e=> Hi @tommathers [github.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_tommathers&d=DwMCaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=MigC00eCez0AYiD8Bi3uR5vUblihAN7OJ3KK8sbnotw&m=w_H3IPxeL55D3gCZzVCMORvLhjZPTTC7XfoC8-QykpUo-qFf6l8FY48mOXuB8unS&s=kjnIOB7Se8X9ogMaf_7IeiZBdC-3Ep1nN6CW0Ym7sdc&e=>, do you agree to review this assembly? Please reply to this message only with Yes or No by 05-Feb-2026 at 17:59 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_343-23issuecomment-2D3823633007&d=DwMCaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=MigC00eCez0AYiD8Bi3uR5vUblihAN7OJ3KK8sbnotw&m=w_H3IPxeL55D3gCZzVCMORvLhjZPTTC7XfoC8-QykpUo-qFf6l8FY48mOXuB8unS&s=JNPs_LpDKLPAERxve19dL2OnEPPdyJPj9ZKnS1cl0Hk&e=>, or unsubscribe [github.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_ABVP3GZ67G6MRQTYRUWKQ434JNIU3AVCNFSM6AAAAACTNSCDBWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTQMRTGYZTGMBQG4&d=DwMCaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=MigC00eCez0AYiD8Bi3uR5vUblihAN7OJ3KK8sbnotw&m=w_H3IPxeL55D3gCZzVCMORvLhjZPTTC7XfoC8-QykpUo-qFf6l8FY48mOXuB8unS&s=pYUxwKg1GA4gFMPW9KSNufJiVk1sO1NN9a9NwV8FKhc&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.

[fcamara7]

@tommathers and @diegomics any comments on this one? Thanks!

[tbrown91]

Hey @fcamara7

This is looking very nice - it helps having most scaffolds in a single contig. I'd be happy to sign this one off

@tommathers @diegomics have a look and see if you agree

[diegomics]

Hi @tommathers have you looked at this one, looks pretty ready to go for me

[tommathers]

Hap 1 looks great and very impressive contiguity!

Hap 2 SUPER_9 has large assembly error. Currently joined at telomeres, need to move chunk from start to gap at 15.5 Mb to the end.

Also, the SUPER IDs don't match between hap1 and hap2 eg. HAP1 SUPER 7 corresponds to HAP2 SUPER_9. Normally when submitting two curated haplotypes we orientate and name HAP2 after HAP1. If curating a merged map this should be done automatically by the pretext-to-asm scipts. Note orientation needs to be done manually in the merged map.