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kaBotViol1 EAR #306

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@ilenia6 ilenia6 commented Dec 12, 2025

Assembly review request

  • ToLID: kaBotViol1
  • Species: Botrylloides violaceus
  • Project: ERGA-BGE
  • Affiliation: UNIBA

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erga-ear-bot bot commented Dec 12, 2025

Hi @ilenia6, thanks for sending the EAR of Botrylloides violaceus.
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 Dec 12, 2025

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

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additive3 commented Dec 12, 2025 via email

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erga-ear-bot bot commented Dec 12, 2025 

*****
EAR Reviewer Selection Process
Date: 2025-12-12 16:25

All Eligible Candidates:

Github ID     | Full Name             | Institution | Total Reviews | Last Review | Active | Working PRs | Calling Score | Adjusted Score
-----------------------------------------------------------------------------------------------------------------------------------------
CaroB-M       | Caroline Menguy       | Genoscope   | 16            | 2025-12-12  | Y      | 0           | 1037          | 1087          
jesgomez      | Jessica Gomez Garrido | CNAG        | 13            | 2025-12-04  | Y      | 1           | 1025          | 1055          
MartinPippel  | Martin Pippel         | SciLifeLab  | 2             | 2025-10-06  | Y      | 1           | 1024          | 1054          
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          
bistace       | Benjamin Istace       | Genoscope   | 10            | 2025-12-10  | Y      | 2           | 1043          | 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          
ldemirdj      | Lola Demirdjian       | Genoscope   | 11            | 2025-10-14  | Y      | 2           | 1041          | 1051          
auryjm        | Jean-Marc Aury        | Genoscope   | 12            | 2025-11-18  | Y      | 2           | 1040          | 1050          
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          
tbrown91      | Tom Brown             | IZW         | 11            | 2025-07-29  | Y      | 1           | 996           | 1021          

Selected reviewer: Caroline Menguy (CaroB-M)
The decision was based on:
- different institution ('Genoscope')
- active ('Y')
- working on 0 PR(s) currently
- highest adjusted calling score in this particular selection (1087)

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erga-ear-bot bot commented Dec 12, 2025

Hi @CaroB-M, do you agree to review this assembly?
Please reply to this message only with Yes or No by 18-Dec-2025 at 21:24 CET

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CaroB-M commented Dec 15, 2025

No

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erga-ear-bot bot commented Dec 15, 2025

@CaroB-M Ok thank you, 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 08:49

All Eligible Candidates:

Github ID     | Full Name             | Institution | Total Reviews | Last Review | Active | Working PRs | Calling Score | Adjusted Score
-----------------------------------------------------------------------------------------------------------------------------------------
jesgomez      | Jessica Gomez Garrido | CNAG        | 13            | 2025-12-04  | Y      | 1           | 1025          | 1055          
MartinPippel  | Martin Pippel         | SciLifeLab  | 2             | 2025-10-06  | Y      | 1           | 1024          | 1054          
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          
bistace       | Benjamin Istace       | Genoscope   | 10            | 2025-12-10  | Y      | 2           | 1043          | 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          
ldemirdj      | Lola Demirdjian       | Genoscope   | 11            | 2025-10-14  | Y      | 2           | 1041          | 1051          
auryjm        | Jean-Marc Aury        | Genoscope   | 12            | 2025-11-18  | Y      | 2           | 1040          | 1050          
additive3     | Jo Wood               | Sanger      | 8             | 2025-10-17  | Y      | 1           | 1022          | 1047          
CaroB-M       | Caroline Menguy       | Genoscope   | 16            | 2025-12-12  | Y      | 2           | 1037          | 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          
tbrown91      | Tom Brown             | IZW         | 11            | 2025-07-29  | Y      | 1           | 996           | 1021          

Selected reviewer: Jessica Gomez Garrido (jesgomez)
The decision was based on:
- different institution ('CNAG')
- active ('Y')
- working on 1 PR(s) currently
- highest adjusted calling score in this particular selection (1055)
  (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 @MartinPippel, do you agree to review this assembly?
Please reply to this message only with Yes or No by 19-Dec-2025 at 13:49 CET

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MartinPippel commented Dec 15, 2025

Yes

@erga-ear-bot erga-ear-bot bot requested a review from MartinPippel December 15, 2025 13:04
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erga-ear-bot bot commented Dec 15, 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.

@MartinPippel
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MartinPippel commented Dec 19, 2025

Hej @ilenia6,

congrats on this assembly. Marine species are usually pretty difficult to assemble and I would expect a lot more contamination. But it looks pretty clean to me. I was a bit surprised that you did not subsample the ONT data further down to <100X. Usually such a high coverages result in assembly issues and bias QV estimates.

I do have a few comments on the assembly:

  • Super_1:
    - gap at 684Kb - very tiny duplication, but probably too small to correct in PretextView
    - gap at 5.04Mb - small duplication
  • Super_4:
    - tandem repeat: 8.0M - 8.4M personally I would order them into a parallel pattern, but not sure if this is correct. What do you think @additive3 ? You might want to add a comment that the order and orientation within this region cannot be 100% confirmed when submitting this assembly to ENA.
image
  • Super_6:
    • I would invert the last contig at: 7.8M - 8.0M
image
  • Super_7:
    • I would invert contig at: 860K - 1200K
image
  • Super_12:
    • I would invert the first 2 contigs: 1 - 811K
image
  • Super_15:
    • similar comment as in SUPER_4 for tandem repeat at 923K - 1026K

There might be some shrapnels that could be assigned to chromosomes or potentially removed because of dups:

  • scaffold_229: last part has signal with SUPER_3, first part has a signal with SUPER_7, both parts want to go into a contig and the coverage is very low - so I would just mark it as dup
  • scaffold_225: signal with SUPER_4 --> duplication
  • scaffold_208: signal with SUPER_7, could be placed into the gap but doesn't look great, maybe mark as unloc?
  • scaffold_242, scaffold_218: signals with SUPER_8 --> duplications
  • scaffold_230, scaffold_228, scaffold_233: signals with SUPER_9 --> duplications
  • maybe add scaffold_60 to the end of SUPER_14 and mark scaffold_61 as duplication

Please let me know what you think.

@ilenia6
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ilenia6 commented Dec 22, 2025

Hi @MartinPippel , thank you very much for all the details and suggestions. I’ll start working on it right away and will let you know as soon as I’m done!

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ilenia6 commented Dec 22, 2025

Ok @MartinPippel , I’ve integrated the changes, thank you so much for your help...regarding the sequences inverted, I must have forgotten to fix them, as they were actually quite obvious. Regarding the interaction between scaffold_208 and SUPER_7, in the end I assigned it at the gap position, and it seems fine to me this way. However, I still have some doubts about how to handle the tandem repeat regions in SUPER_4 and SUPER_15. I tried to arrange them along parallel lines, but I’m not entirely sure this works correctly. Do you (or @additive3 ) have any other suggestions on this? They would be very helpful.

Thank you again!

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erga-ear-bot bot commented Dec 29, 2025

Ping @additive3,
One week without any movements on this PR!

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erga-ear-bot bot commented Jan 5, 2026

Ping @additive3,
One week without any movements on this PR!

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