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heEubCras1 EAR - #402

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heEubCras1 EAR#402
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epaule:heEubCras1_EAR

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@epaule

@epaule epaule commented Aug 7, 2026

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Assembly review request

  • ToLID: heEubCras1
  • Species: Eubothrium crassum
  • Project: ERGA-BGE
  • Affiliation: Sanger

@erga-ear-bot

erga-ear-bot Bot commented Aug 7, 2026

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Hi @epaule, thanks for sending the EAR of Eubothrium crassum.
I added the corresponding tag to the PR and will contact a supervisor and a reviewer ASAP.

@erga-ear-bot erga-ear-bot Bot added the ERGA-BGE label Aug 7, 2026
@erga-ear-bot

erga-ear-bot Bot commented Aug 7, 2026

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

@diegomics

diegomics commented Aug 7, 2026

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Ok

@erga-ear-bot

erga-ear-bot Bot commented Aug 7, 2026

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*****
EAR Reviewer Selection Process
Date: 2026-08-07 18:35

All Eligible Candidates:

Github ID    | Full Name             | Institution | Total Reviews | Last Review | Active | Working PRs | Calling Score | Adjusted Score
----------------------------------------------------------------------------------------------------------------------------------------
auryjm       | Jean-Marc Aury        | Genoscope   | 18            | 2026-07-24  | Y      | 0           | 1043          | 1093          
EmilieTeo    | Emilie Teodori        | Genoscope   | 21            | 2026-06-05  | Y      | 0           | 1040          | 1090          
jesgomez     | Jessica Gomez Garrido | CNAG        | 20            | 2026-07-06  | Y      | 0           | 1039          | 1089          
MartinPippel | Martin Pippel         | SciLifeLab  | 7             | 2026-07-24  | Y      | 0           | 1031          | 1081          
gbdias       | Guilherme Dias        | SciLifeLab  | 9             | 2026-04-23  | Y      | 0           | 1029          | 1079          
bistace      | Benjamin Istace       | Genoscope   | 17            | 2026-04-22  | Y      | 1           | 1045          | 1075          
talioto      | Tyler Alioto          | CNAG        | 10            | 2026-02-20  | Y      | 2           | 1048          | 1058          
msozzoni     | Marcella Sozzoni      | UNIFI       | 3             | 2026-02-19  | Y      | 0           | 1007          | 1057          
gitcruz      | Fernando Cruz         | CNAG        | 17            | 2026-06-05  | Y      | 2           | 1043          | 1053          
diegomics    | Diego De Panis        | IZW         | 11            | 2025-09-22  | Y      | 0           | 997           | 1042          

Selected reviewer: Jean-Marc Aury (auryjm)
The decision was based on:
- different institution ('Genoscope')
- active ('Y')
- working on 0 PR(s) currently
- highest adjusted calling score in this particular selection (1093)

@erga-ear-bot

erga-ear-bot Bot commented Aug 7, 2026

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Hi @auryjm, do you agree to review this assembly?
Please reply to this message only with Yes or No by 14-Aug-2026 at 00:35 CET

@erga-ear-bot

erga-ear-bot Bot commented Aug 14, 2026

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@auryjm Time is out! I will look for the next reviewer on the list :)

@erga-ear-bot

erga-ear-bot Bot commented Aug 14, 2026

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*****
EAR Reviewer Selection Process
Date: 2026-08-14 10:00

All Eligible Candidates:

Github ID    | Full Name             | Institution | Total Reviews | Last Review | Active | Working PRs | Calling Score | Adjusted Score
----------------------------------------------------------------------------------------------------------------------------------------
EmilieTeo    | Emilie Teodori        | Genoscope   | 21            | 2026-06-05  | Y      | 0           | 1040          | 1090          
jesgomez     | Jessica Gomez Garrido | CNAG        | 20            | 2026-07-06  | Y      | 0           | 1039          | 1089          
MartinPippel | Martin Pippel         | SciLifeLab  | 7             | 2026-07-24  | Y      | 0           | 1032          | 1082          
gbdias       | Guilherme Dias        | SciLifeLab  | 9             | 2026-04-23  | Y      | 0           | 1030          | 1080          
bistace      | Benjamin Istace       | Genoscope   | 17            | 2026-04-22  | Y      | 1           | 1045          | 1075          
auryjm       | Jean-Marc Aury        | Genoscope   | 18            | 2026-07-24  | Y      | 1           | 1043          | 1073          
talioto      | Tyler Alioto          | CNAG        | 10            | 2026-02-20  | Y      | 2           | 1048          | 1058          
msozzoni     | Marcella Sozzoni      | UNIFI       | 3             | 2026-02-19  | Y      | 0           | 1007          | 1057          
gitcruz      | Fernando Cruz         | CNAG        | 17            | 2026-06-05  | Y      | 2           | 1043          | 1053          
diegomics    | Diego De Panis        | IZW         | 11            | 2025-09-22  | Y      | 0           | 997           | 1042          

Selected reviewer: Emilie Teodori (EmilieTeo)
The decision was based on:
- different institution ('Genoscope')
- active ('Y')
- working on 0 PR(s) currently
- highest adjusted calling score in this particular selection (1090)

@erga-ear-bot

erga-ear-bot Bot commented Aug 14, 2026

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Hi @EmilieTeo, do you agree to review this assembly?
Please reply to this message only with Yes or No by 20-Aug-2026 at 15:59 CET

@erga-ear-bot

erga-ear-bot Bot commented Aug 14, 2026

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

@erga-ear-bot

erga-ear-bot Bot commented Aug 20, 2026

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@EmilieTeo Time is out! I will look for the next reviewer on the list :)

@erga-ear-bot

erga-ear-bot Bot commented Aug 20, 2026

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*****
EAR Reviewer Selection Process
Date: 2026-08-20 21:26

All Eligible Candidates:

Github ID    | Full Name             | Institution | Total Reviews | Last Review | Active | Working PRs | Calling Score | Adjusted Score
----------------------------------------------------------------------------------------------------------------------------------------
jesgomez     | Jessica Gomez Garrido | CNAG        | 20            | 2026-07-06  | Y      | 0           | 1039          | 1089          
MartinPippel | Martin Pippel         | SciLifeLab  | 7             | 2026-07-24  | Y      | 0           | 1032          | 1082          
gbdias       | Guilherme Dias        | SciLifeLab  | 9             | 2026-04-23  | Y      | 0           | 1030          | 1080          
bistace      | Benjamin Istace       | Genoscope   | 17            | 2026-04-22  | Y      | 1           | 1045          | 1075          
auryjm       | Jean-Marc Aury        | Genoscope   | 18            | 2026-07-24  | Y      | 1           | 1043          | 1073          
EmilieTeo    | Emilie Teodori        | Genoscope   | 21            | 2026-06-05  | Y      | 1           | 1040          | 1070          
talioto      | Tyler Alioto          | CNAG        | 10            | 2026-02-20  | Y      | 2           | 1048          | 1058          
msozzoni     | Marcella Sozzoni      | UNIFI       | 3             | 2026-02-19  | Y      | 0           | 1007          | 1057          
gitcruz      | Fernando Cruz         | CNAG        | 17            | 2026-06-05  | Y      | 2           | 1043          | 1053          
diegomics    | Diego De Panis        | IZW         | 11            | 2025-09-22  | Y      | 0           | 997           | 1042          

Selected reviewer: Jessica Gomez Garrido (jesgomez)
The decision was based on:
- different institution ('CNAG')
- active ('Y')
- working on 0 PR(s) currently
- highest adjusted calling score in this particular selection (1089)

@erga-ear-bot

erga-ear-bot Bot commented Aug 20, 2026

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Hi @jesgomez, do you agree to review this assembly?
Please reply to this message only with Yes or No by 27-Aug-2026 at 03:26 CET

@erga-ear-bot

erga-ear-bot Bot commented Aug 22, 2026

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

@diegomics

diegomics commented Aug 27, 2026

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Very useful curation notes, thanks!
In the meantime a reviewer accepts this, I did a quick pass and looks ok for me, some spots like SUPER_1_HAP_1 48,875-49,471 Kbp look a little bit odd but changing it doesn't seem to improve it.

@erga-ear-bot

erga-ear-bot Bot commented Aug 27, 2026

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@jesgomez Time is out! I will look for the next reviewer on the list :)

@erga-ear-bot

erga-ear-bot Bot commented Aug 27, 2026

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*****
EAR Reviewer Selection Process
Date: 2026-08-27 19:27

All Eligible Candidates:

Github ID    | Full Name             | Institution | Total Reviews | Last Review | Active | Working PRs | Calling Score | Adjusted Score
----------------------------------------------------------------------------------------------------------------------------------------
MartinPippel | Martin Pippel         | SciLifeLab  | 7             | 2026-07-24  | Y      | 0           | 1032          | 1082          
gbdias       | Guilherme Dias        | SciLifeLab  | 9             | 2026-04-23  | Y      | 0           | 1030          | 1080          
bistace      | Benjamin Istace       | Genoscope   | 17            | 2026-04-22  | Y      | 1           | 1045          | 1075          
auryjm       | Jean-Marc Aury        | Genoscope   | 18            | 2026-07-24  | Y      | 1           | 1043          | 1073          
EmilieTeo    | Emilie Teodori        | Genoscope   | 21            | 2026-06-05  | Y      | 1           | 1040          | 1070          
jesgomez     | Jessica Gomez Garrido | CNAG        | 20            | 2026-07-06  | Y      | 1           | 1039          | 1069          
talioto      | Tyler Alioto          | CNAG        | 10            | 2026-02-20  | Y      | 2           | 1048          | 1058          
msozzoni     | Marcella Sozzoni      | UNIFI       | 3             | 2026-02-19  | Y      | 0           | 1007          | 1057          
gitcruz      | Fernando Cruz         | CNAG        | 17            | 2026-06-05  | Y      | 2           | 1043          | 1053          
diegomics    | Diego De Panis        | IZW         | 11            | 2025-09-22  | Y      | 0           | 997           | 1042          

Selected reviewer: Martin Pippel (MartinPippel)
The decision was based on:
- different institution ('SciLifeLab')
- active ('Y')
- working on 0 PR(s) currently
- highest adjusted calling score in this particular selection (1082)

@erga-ear-bot

erga-ear-bot Bot commented Aug 27, 2026

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Hi @MartinPippel, do you agree to review this assembly?
Please reply to this message only with Yes or No by 03-Sep-2026 at 01:26 CET

@MartinPippel

MartinPippel commented Aug 28, 2026

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Yes

@erga-ear-bot
erga-ear-bot Bot requested a review from MartinPippel August 28, 2026 04:27
@erga-ear-bot

erga-ear-bot Bot commented Aug 28, 2026

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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.

@MartinPippel

MartinPippel commented Aug 31, 2026

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Hi @epaule,

wow, that curation must have a been a lot of work! Congrats, it looks really good.
I do have some suggestions/questions mainly based on the coverage track. Though I don't know how trustworthy this is.

SUP_1_HP1: gap at 43.47 small dup?
SUP_1_HP1: 45.0M - 46.5M the region that Diego mentioned looks also odd to me. Don't know if cutting out this region would solves it. Are there any busco gene dups in that area?
SUP_1_HP1: 53.0M - 53.2M small dup
SUP_1_HP1: 106.7M small dup?
SUP_1_HP1: 286.35M - 286.7 small dup

You already assigned some unlocalized contigs/scaffolds to SUP_1_HP1. But I think there are probably more. e.g.:
3135, 3077,3448,2347,2978,1580,1846,1997, 2372, ... Some of them are potentially dups and others e.g. 1358 or 1400 show some scaffolding errors, as only parts match with SUP_1_HP1.

SUP_2_HP1: 110.6M - 110.7M small dup
SUP_2_HP1: 199.5M - 199.8M small dup

some more unlocalized/dups ones: 2452, 1432, 3357, 3050, 2427, 2440, 2399, 1073, 1504, ...

SUP_3_HP1: 10.2M - 10.3M --> SUP_1_HP1 23.84M (unlocalized/dup of SUP_1_HP1)
some more unlocalized ones

SUP_4_HP1: 26.8M - 26.9M is probably a dup in SUP_4_HP1: 23.7M (which is probably a dup as well 23.4 - 23.7 vs 23.7 - 24.1, though just from coverage, not from the HiC-signal)
SUP_4_HP1: 56.0M - 56.2M small dup
SUP_4_HP1: 55.0M - 56.0M a dup in (56.2 - 56.7M) ?
SUP_4_HP1: 56.0M - 56.2M small dup
SUP_4_HP1: 60.4M - 60.8M small dup
SUP_4_HP1: 74.6M - 74.8M small dup i

some more unlocalized ones ?

SUP_5_HP1: 89.2M - 91.5M dup
SUP_5_HP1: 92.9M - 93.3M small dup
SUP_5_HP1: 97.5M - 97.7M small dup
SUP_5_HP1: 98.2M - 99.1M inversion?

some more unlocalized ones ?

SUP_6_HP1: 56.8M - 57.2M inversion (and partial dup) ?
SUP_6_HP1: 72.7M - 73.1M small dup

some more unlocalized ones ?
SUP_7_HP1: 9.0M - 9.5M small dup
SUP_7_HP1: 21.7M - 22.2gM small dup

Plz have a look and let me know what you think.

@erga-ear-bot erga-ear-bot Bot added the DELAYED label Sep 4, 2026
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