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ilManCypr1 EAR#337

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fcamara7 wants to merge 2 commits intoERGA-consortium:mainfrom
fcamara7:fcamara7-ilManCypr1_EAR
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ilManCypr1 EAR#337
fcamara7 wants to merge 2 commits intoERGA-consortium:mainfrom
fcamara7:fcamara7-ilManCypr1_EAR

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@fcamara7
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@fcamara7 fcamara7 commented Jan 26, 2026

Assembly review request

  • ToLID: ilManCypr1
  • Species: Maniola cypricola
  • Project: ERGA-BGE
  • Affiliation: CNAG

@fcamara7
ilManCypr1 EAR
ccb2053 
Species: Maniola cypricola
Taxa: Lepidoptera
Project: ERGA-BGE
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erga-ear-bot bot commented Jan 26, 2026

Hi @fcamara7, thanks for sending the EAR of Maniola cypricola.
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 Jan 26, 2026

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

@additive3
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additive3 commented Jan 26, 2026 via email

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erga-ear-bot bot commented Jan 26, 2026 

*****
EAR Reviewer Selection Process
Date: 2026-01-26 14:18

All Eligible Candidates:

Github ID     | Full Name        | Institution | Total Reviews | Last Review | Active | Working PRs | Calling Score | Adjusted Score
------------------------------------------------------------------------------------------------------------------------------------
CaroB-M       | Caroline Menguy  | Genoscope   | 17            | 2026-01-20  | Y      | 1           | 1039          | 1069          
msozzoni      | Marcella Sozzoni | UNIFI       | 0             | NA          | Y      | 2           | 1006          | 1066          
MartinPippel  | Martin Pippel    | SciLifeLab  | 3             | 2026-01-20  | Y      | 1           | 1027          | 1057          
gbdias        | Guilherme Dias   | SciLifeLab  | 6             | 2026-01-23  | Y      | 1           | 1024          | 1054          
tommathers    | Tom Mathers      | Sanger      | 7             | 2025-10-16  | Y      | 1           | 1024          | 1054          
joannacollins | Jo Collins       | Sanger      | 7             | 2026-01-16  | Y      | 1           | 1024          | 1054          
bistace       | Benjamin Istace  | Genoscope   | 12            | 2026-01-21  | Y      | 2           | 1044          | 1054          
DomAbsolon    | Dom Absolon      | Sanger      | 8             | 2025-11-04  | Y      | 1           | 1023          | 1053          
ldemirdj      | Lola Demirdjian  | Genoscope   | 12            | 2026-01-20  | Y      | 2           | 1043          | 1053          
auryjm        | Jean-Marc Aury   | Genoscope   | 13            | 2026-01-20  | Y      | 2           | 1042          | 1052          
EmilieTeo     | Emilie Teodori   | Genoscope   | 15            | 2025-12-15  | Y      | 2           | 1040          | 1050          
additive3     | Jo Wood          | Sanger      | 8             | 2025-10-17  | Y      | 1           | 1023          | 1048          
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          
SarahPelan    | Sarah Pelan      | Sanger      | 7             | 2025-12-19  | Y      | 2           | 1024          | 1034          

Selected reviewer: Caroline Menguy (CaroB-M)
The decision was based on:
- different institution ('Genoscope')
- active ('Y')
- working on 1 PR(s) currently
- highest adjusted calling score in this particular selection (1069)
  (Note: Adjusted score already considering -20 points due to 1 ongoing PR(s))

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erga-ear-bot bot commented Jan 26, 2026

Hi @CaroB-M, do you agree to review this assembly?
Please reply to this message only with Yes or No by 30-Jan-2026 at 19:18 CET

@additive3
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additive3 commented Jan 26, 2026

Hi @fcamara7

Thanks for the assembly, sounds like it was problematic to produce.
I've identified quite a number of scaffold errors and retained haplotypic duplication.
Lots of haptigs in the small tail of contigs too.

Attaching a savestate with rearragements, I've used waypoint marks to indicate where hapdup needs removing.

ilManCypr.curated_primary.no_mt.scrubbed.mod_mq0.extensions.pretext.savestate_jmdw.txt

@CaroB-M
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CaroB-M commented Jan 28, 2026

yes

@erga-ear-bot erga-ear-bot bot requested a review from CaroB-M January 28, 2026 10:05
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erga-ear-bot bot commented Jan 28, 2026

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
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fcamara7 commented Jan 28, 2026

Hi @fcamara7

Thanks for the assembly, sounds like it was problematic to produce. I've identified quite a number of scaffold errors and retained haplotypic duplication. Lots of haptigs in the small tail of contigs too.

Attaching a savestate with rearragements, I've used waypoint marks to indicate where hapdup needs removing.

ilManCypr.curated_primary.no_mt.scrubbed.mod_mq0.extensions.pretext.savestate_jmdw.txt

Thanks @additive3 I will take a look and make the recommended changes.

@CaroB-M
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CaroB-M commented Jan 28, 2026

Hello,

I agree with the points raised by @additive3.
I added some additionnal waypoints to the savestate.
SUPER_3 HAP at 14,691 and 15,124 (gap + ccoverage drop)
SUPER_6 HAP at 1,407 (gap + ccoverage drop)

sc130 added at the beginning of SUPER_27
sc170 added at the beginning of SUPER_20
sc116 hap of SUPER_20
sc143 hap of SUPER_17
sc169 unloc of SUPER_15
sc165 + sc163 added at 11454Kb
sc95 hap of SUPER_8
sc129 added at the end of SUPER_8
sc107 hap of SUPER_6
sc120 unloc of SUPER_5
sc113 added at 10,612Kb of SUPER_Z
sc101, sc92, sc174 unloc of SUPER_Z
sc102 and sc111 unloc du SUPER_1
ilManCypr.curated_primary.no_mt.scrubbed.mod_mq0.extensions.pretext.savestate_CB.txt

Best
Caroline

@fcamara7
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fcamara7 commented Jan 29, 2026

Hello,

I agree with the points raised by @additive3. I added some additionnal waypoints to the savestate. SUPER_3 HAP at 14,691 and 15,124 (gap + ccoverage drop) SUPER_6 HAP at 1,407 (gap + ccoverage drop)

sc130 added at the beginning of SUPER_27 sc170 added at the beginning of SUPER_20 sc116 hap of SUPER_20 sc143 hap of SUPER_17 sc169 unloc of SUPER_15 sc165 + sc163 added at 11454Kb sc95 hap of SUPER_8 sc129 added at the end of SUPER_8 sc107 hap of SUPER_6 sc120 unloc of SUPER_5 sc113 added at 10,612Kb of SUPER_Z sc101, sc92, sc174 unloc of SUPER_Z sc102 and sc111 unloc du SUPER_1 ilManCypr.curated_primary.no_mt.scrubbed.mod_mq0.extensions.pretext.savestate_CB.txt

Best Caroline

Thanks a lot to both @additive3 and @CaroB-M , I will load @CaroB-M save_state since it seems to include @additive3 suggestions, and I will update my submission asap..Best, Francisco

@fcamara7
ilManCypr1_EAR rev1
dcdbda2 
Species: Maniola cypricola
Taxa: Lepidoptera
Project: ERGA-BGE
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erga-ear-bot bot commented Feb 4, 2026

Attention @CaroB-M, the EAR PDF was updated.

@additive3
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additive3 commented Feb 4, 2026

Hi @fcamara7 @CaroB-M

There is a small haptig remaining at the end of SUPER_1 (also the chrm are now not size ordered) 8.64Mb-end.

I note the sample is female but no W identified, were Hi-C generated from different individual? Might want to mention that W not identified in EAR.

@fcamara7
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fcamara7 commented Feb 4, 2026

Hi @additive3 , thanks! Yes I tagged that haplotig and will remove it before submitting a new EAR. I think a mentioned it briefly in the comments section, but unfortunately we were not able to recover the W for this individual. I believe the HIFI and HiC data come from different individuals. The HiC data came from SciLife for this one.

@CaroB-M
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CaroB-M commented Feb 4, 2026

Hello @fcamara7
I have nothing to add! I am approving the request now because I will be unavailable for a few days.
Best
Caroline

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erga-ear-bot bot commented Feb 4, 2026

Thanks @CaroB-M for the review.
I will add a new reviewed species for you to the table when @additive3 merges the PR ;)

Congrats on the assembly @fcamara7!
Please make sure that the fasta file to upload to ENA is generated based on the final reviewed version of the assembly.

After @additive3 confirmation, you can start with the assembly submission to save time.
The PR will be merged only when the final version of the EAR pdf is available.

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