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Add Arachnocephalus vestitus #286

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@CaroB-M CaroB-M commented Nov 25, 2025

Assembly review request

  • ToLID: iqAraVest5
  • Species: Arachnocephalus vestitus
  • Project: ERGA-BGE
  • Affiliation: Genoscope

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erga-ear-bot bot commented Nov 25, 2025

Attention @CaroB-M, you have changed more than one file!
Please make sure to update only the EAR PDF file.

@erga-ear-bot erga-ear-bot bot added the ERROR! label Nov 25, 2025
@erga-ear-bot erga-ear-bot bot removed the ERROR! label Nov 25, 2025
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erga-ear-bot bot commented Nov 25, 2025

Hi @CaroB-M, thanks for sending the EAR of Arachnocephalus vestitus.
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 Nov 25, 2025

Hi @tbrown91, do you agree to supervise this assembly?
Please reply to this message only with OK to give acknowledge.

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tbrown91 commented Nov 25, 2025

ok

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erga-ear-bot bot commented Nov 25, 2025 

*****
EAR Reviewer Selection Process
Date: 2025-11-25 11:27

All Eligible Candidates:

Github ID     | Full Name             | Institution | Total Reviews | Last Review | Active | Working PRs | Calling Score | Adjusted Score
-----------------------------------------------------------------------------------------------------------------------------------------
gbdias        | Guilherme Dias        | SciLifeLab  | 4             | 2025-11-19  | Y      | 0           | 1017          | 1067          
DomAbsolon    | Dom Absolon           | Sanger      | 8             | 2025-11-04  | Y      | 0           | 1017          | 1067          
talioto       | Tyler Alioto          | CNAG        | 8             | 2025-10-21  | Y      | 1           | 1029          | 1059          
jesgomez      | Jessica Gomez Garrido | CNAG        | 11            | 2025-11-10  | Y      | 1           | 1027          | 1057          
gitcruz       | Fernando Cruz         | CNAG        | 13            | 2025-11-17  | Y      | 1           | 1025          | 1055          
MartinPippel  | Martin Pippel         | SciLifeLab  | 2             | 2025-10-06  | Y      | 1           | 1019          | 1049          
SarahPelan    | Sarah Pelan           | Sanger      | 6             | 2025-09-16  | Y      | 1           | 1019          | 1049          
joannacollins | Jo Collins            | Sanger      | 6             | 2025-10-10  | Y      | 1           | 1019          | 1049          
tommathers    | Tom Mathers           | Sanger      | 7             | 2025-10-16  | Y      | 1           | 1018          | 1048          
diegomics     | Diego De Panis        | IZW         | 11            | 2025-09-22  | Y      | 0           | 992           | 1037          
tbrown91      | Tom Brown             | IZW         | 11            | 2025-07-29  | Y      | 1           | 995           | 1020          

Selected reviewer: Guilherme Dias (gbdias)
The decision was based on:
- different institution ('SciLifeLab')
- active ('Y')
- working on 0 PR(s) currently
- oldest review and fewest reviews among the finalists (1067)

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erga-ear-bot bot commented Nov 25, 2025

Hi @gbdias, do you agree to review this assembly?
Please reply to this message only with Yes or No by 01-Dec-2025 at 16:27 CET

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erga-ear-bot bot commented Dec 1, 2025

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

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erga-ear-bot bot commented Dec 1, 2025 

*****
EAR Reviewer Selection Process
Date: 2025-12-01 21:17

All Eligible Candidates:

Github ID     | Full Name             | Institution | Total Reviews | Last Review | Active | Working PRs | Calling Score | Adjusted Score
-----------------------------------------------------------------------------------------------------------------------------------------
gitcruz       | Fernando Cruz         | CNAG        | 13            | 2025-11-17  | Y      | 0           | 1025          | 1075          
MartinPippel  | Martin Pippel         | SciLifeLab  | 2             | 2025-10-06  | Y      | 1           | 1022          | 1052          
gbdias        | Guilherme Dias        | SciLifeLab  | 4             | 2025-11-19  | Y      | 1           | 1020          | 1050          
SarahPelan    | Sarah Pelan           | Sanger      | 6             | 2025-09-16  | Y      | 1           | 1019          | 1049          
joannacollins | Jo Collins            | Sanger      | 6             | 2025-10-10  | Y      | 1           | 1019          | 1049          
tommathers    | Tom Mathers           | Sanger      | 7             | 2025-10-16  | Y      | 1           | 1018          | 1048          
DomAbsolon    | Dom Absolon           | Sanger      | 8             | 2025-11-04  | Y      | 1           | 1017          | 1047          
additive3     | Jo Wood               | Sanger      | 8             | 2025-10-17  | Y      | 1           | 1017          | 1042          
talioto       | Tyler Alioto          | CNAG        | 8             | 2025-10-21  | Y      | 2           | 1029          | 1039          
diegomics     | Diego De Panis        | IZW         | 11            | 2025-09-22  | Y      | 0           | 992           | 1037          
jesgomez      | Jessica Gomez Garrido | CNAG        | 12            | 2025-11-26  | Y      | 2           | 1026          | 1036          
tbrown91      | Tom Brown             | IZW         | 11            | 2025-07-29  | Y      | 1           | 995           | 1020          

Selected reviewer: Fernando Cruz (gitcruz)
The decision was based on:
- different institution ('CNAG')
- active ('Y')
- working on 0 PR(s) currently
- highest adjusted calling score in this particular selection (1075)

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erga-ear-bot bot commented Dec 1, 2025

Hi @gitcruz, do you agree to review this assembly?
Please reply to this message only with Yes or No by 08-Dec-2025 at 02:16 CET

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gitcruz commented Dec 2, 2025

No

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erga-ear-bot bot commented Dec 2, 2025

@gitcruz Ok thank you, I will look for the next reviewer on the list :)

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erga-ear-bot bot commented Dec 2, 2025 

*****
EAR Reviewer Selection Process
Date: 2025-12-02 10:46

All Eligible Candidates:

Github ID     | Full Name             | Institution | Total Reviews | Last Review | Active | Working PRs | Calling Score | Adjusted Score
-----------------------------------------------------------------------------------------------------------------------------------------
gitcruz       | Fernando Cruz         | CNAG        | 13            | 2025-11-17  | Y      | 0           | 1025          | 1075          
MartinPippel  | Martin Pippel         | SciLifeLab  | 2             | 2025-10-06  | Y      | 1           | 1023          | 1053          
gbdias        | Guilherme Dias        | SciLifeLab  | 4             | 2025-11-19  | Y      | 1           | 1021          | 1051          
SarahPelan    | Sarah Pelan           | Sanger      | 6             | 2025-09-16  | Y      | 1           | 1019          | 1049          
joannacollins | Jo Collins            | Sanger      | 6             | 2025-10-10  | Y      | 1           | 1019          | 1049          
tommathers    | Tom Mathers           | Sanger      | 7             | 2025-10-16  | Y      | 1           | 1018          | 1048          
DomAbsolon    | Dom Absolon           | Sanger      | 8             | 2025-11-04  | Y      | 1           | 1017          | 1047          
additive3     | Jo Wood               | Sanger      | 8             | 2025-10-17  | Y      | 1           | 1017          | 1042          
talioto       | Tyler Alioto          | CNAG        | 8             | 2025-10-21  | Y      | 2           | 1029          | 1039          
diegomics     | Diego De Panis        | IZW         | 11            | 2025-09-22  | Y      | 0           | 992           | 1037          
jesgomez      | Jessica Gomez Garrido | CNAG        | 12            | 2025-11-26  | Y      | 2           | 1026          | 1036          
tbrown91      | Tom Brown             | IZW         | 11            | 2025-07-29  | Y      | 1           | 995           | 1020          

Selected reviewer: Fernando Cruz (gitcruz)
The decision was based on:
- different institution ('CNAG')
- active ('Y')
- working on 0 PR(s) currently
- highest adjusted calling score in this particular selection (1075)

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erga-ear-bot bot commented Dec 2, 2025

Hi @gitcruz, do you agree to review this assembly?
Please reply to this message only with Yes or No by 08-Dec-2025 at 15:46 CET

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tbrown91 commented Dec 2, 2025

@diegomics not sure what's going on here

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erga-ear-bot bot commented Dec 8, 2025

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

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erga-ear-bot bot commented Dec 8, 2025 

*****
EAR Reviewer Selection Process
Date: 2025-12-08 21:17

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           | 1020          | 1070          
gitcruz       | Fernando Cruz         | CNAG        | 13            | 2025-11-17  | Y      | 1           | 1025          | 1055          
jesgomez      | Jessica Gomez Garrido | CNAG        | 13            | 2025-12-04  | Y      | 1           | 1025          | 1055          
MartinPippel  | Martin Pippel         | SciLifeLab  | 2             | 2025-10-06  | Y      | 1           | 1023          | 1053          
SarahPelan    | Sarah Pelan           | Sanger      | 6             | 2025-09-16  | Y      | 1           | 1022          | 1052          
joannacollins | Jo Collins            | Sanger      | 6             | 2025-10-10  | Y      | 1           | 1022          | 1052          
gbdias        | Guilherme Dias        | SciLifeLab  | 4             | 2025-11-19  | Y      | 1           | 1021          | 1051          
tommathers    | Tom Mathers           | Sanger      | 7             | 2025-10-16  | Y      | 1           | 1021          | 1051          
additive3     | Jo Wood               | Sanger      | 8             | 2025-10-17  | Y      | 1           | 1020          | 1045          
talioto       | Tyler Alioto          | CNAG        | 8             | 2025-10-21  | Y      | 2           | 1029          | 1039          
diegomics     | Diego De Panis        | IZW         | 11            | 2025-09-22  | Y      | 0           | 993           | 1038          
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 (1070)

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erga-ear-bot bot commented Dec 8, 2025

Hi @gitcruz, do you agree to review this assembly?
Please reply to this message only with Yes or No by 15-Dec-2025 at 02:17 CET

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gbdias commented Dec 9, 2025

I was teaching and missed the initial review assignment. Now I am able to review it if you want to assign it to me @tbrown91

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diegomics commented Dec 9, 2025

Sorry I missed this, let me see what's going on...

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erga-ear-bot bot commented Dec 15, 2025

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

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erga-ear-bot bot commented Dec 15, 2025 

*****
EAR Reviewer Selection Process
Date: 2025-12-15 09:34

All Eligible Candidates:

Github ID     | Full Name             | Institution | Total Reviews | Last Review | Active | Working PRs | Calling Score | Adjusted Score
-----------------------------------------------------------------------------------------------------------------------------------------
SarahPelan    | Sarah Pelan           | Sanger      | 6             | 2025-09-16  | Y      | 1           | 1024          | 1054          
joannacollins | Jo Collins            | Sanger      | 6             | 2025-10-10  | Y      | 1           | 1024          | 1054          
tommathers    | Tom Mathers           | Sanger      | 7             | 2025-10-16  | Y      | 1           | 1023          | 1053          
gbdias        | Guilherme Dias        | SciLifeLab  | 4             | 2025-11-19  | Y      | 1           | 1022          | 1052          
DomAbsolon    | Dom Absolon           | Sanger      | 8             | 2025-11-04  | Y      | 1           | 1022          | 1052          
additive3     | Jo Wood               | Sanger      | 8             | 2025-10-17  | Y      | 1           | 1022          | 1047          
talioto       | Tyler Alioto          | CNAG        | 8             | 2025-10-21  | Y      | 2           | 1029          | 1039          
diegomics     | Diego De Panis        | IZW         | 11            | 2025-09-22  | Y      | 0           | 993           | 1038          
gitcruz       | Fernando Cruz         | CNAG        | 13            | 2025-11-17  | Y      | 2           | 1025          | 1035          
jesgomez      | Jessica Gomez Garrido | CNAG        | 13            | 2025-12-04  | Y      | 2           | 1025          | 1035          
MartinPippel  | Martin Pippel         | SciLifeLab  | 2             | 2025-10-06  | Y      | 2           | 1024          | 1034          
tbrown91      | Tom Brown             | IZW         | 11            | 2025-07-29  | Y      | 1           | 996           | 1021          

Selected reviewer: Sarah Pelan (SarahPelan)
The decision was based on:
- different institution ('Sanger')
- active ('Y')
- working on 1 PR(s) currently
- oldest review and fewest reviews among the finalists (1054)
  (Note: Adjusted score already considering -20 points due to 1 ongoing PR(s))

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erga-ear-bot bot commented Dec 15, 2025

Hi @JoannaCollins, do you agree to review this assembly?
Please reply to this message only with Yes or No by 19-Dec-2025 at 14:31 CET

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erga-ear-bot bot commented Dec 16, 2025

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

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JoannaCollins commented Dec 16, 2025

yes

@erga-ear-bot erga-ear-bot bot requested a review from JoannaCollins December 16, 2025 12:31
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erga-ear-bot bot commented Dec 16, 2025

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.

JoannaCollins
JoannaCollins requested changes Dec 19, 2025
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Hi @CaroB-M

Great Job with this genome, I have now completed the QC and there are some regions to update.

Please let me know if there are any questions.

Have a great weekend

Best Wishes, Jo.

Chr1: Haplotypic duplication @ 374.40

Chr2:region @ 98.05 looks to belong @ 109.36.

Chr3: I think some of the repeat @ 30.06-43.58 potentially belongs on other chrs. its quite difficult to determine with any confidence what goes where though. I think i would be tempted to move the region 37.08-43.53 to chr 4 @ 45.93 though. Unlocs 1 and 3 belong on chr 8.

Chr5: only gapped one side but 20.73-22.76 looks like it needs to flip. 147.52-148.46 looks to flip.

Chr7: 7.16-7.35 belongs on chr 9 @ 138.43. The same is true for 18.28-18.42. 53.38-54.27 looks to flip. 178.71-178.81 looks to belong on chr2 @ 228.72. 226.65-221.79 belongs in the gap @ 221.83. 221.80-212.07 belongs in the gap @ 232.99. 249.96-end hits the ends of many chrs so i think i would unassign this piece.

Chr8: 8.29-8.52 looks to go in the gap @ 7.49. Region is very gappy so tricky to determine true order but 223.15-223.57 looks to go in the gap @ 224.61.

Chr9: 116.66-116.85 looks like it belongs @ 114.96. Unlocs 2 and 3 look to belong on chr7. Unloc 4 mathches multiple chrs so it might be best to unassign. I would place unloc_1 in the gap @ 35.71 in the -ve orientation.

Chr10: 186.49-187.24 looks to flip and go in the gap @ 187.85. 74.72-74.96 looks like it might be a duplicate of the region around 86.60 looking at cov.

@erga-ear-bot erga-ear-bot bot added the DELAYED label Dec 23, 2025
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erga-ear-bot bot commented Dec 23, 2025

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

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CaroB-M commented Jan 6, 2026

Hi @JoannaCollins
I wish you a happy new year!
Thanks a lot for your review. I did all the changes except for chr7 :
Chr7: 7.16-7.35 belongs on chr 9 @ 138.43 --> OK done
The same is true for 18.28-18.42 --> OK done.
53.38-54.27 looks to flip --> OK done
178.71-178.81 looks to belong on chr2 @ 228.72 --> I let it as it. Not sure it looks better on chr2
226.65-221.79 belongs in the gap @ 221.83 --> I let it as it. Could you send me a picture of this region because I don't know how to change it
221.80-212.07 belongs in the gap @ 232.99 --> I let it as it. Could you send me a picture of this region because I don't know how to change it
249.96-end hits the ends of many chrs so i think i would unassign this piece. --> OK done

best
Caroline

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