xgSipPect3 EAR

[Estel-Kitsune]

Assembly review request

• ToLID: xgSipPect3
• Species: Siphonaria pectinata
• Project: ERGA-BGE
• Affiliation: SciLifeLab

[erga-ear-bot]

Hi @Estel-Kitsune, thanks for sending the EAR of Siphonaria pectinata.
I added the corresponding tag to the PR and will contact a supervisor and a reviewer ASAP.

[erga-ear-bot]

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

[tbrown91]

ok

[erga-ear-bot]

*****
EAR Reviewer Selection Process
Date: 2025-11-26 08:55

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           | 1017          | 1067          
additive3     | Jo Wood               | Sanger      | 8             | 2025-10-17  | Y      | 0           | 1017          | 1062          
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          
bistace       | Benjamin Istace       | Genoscope   | 7             | 2025-10-17  | Y      | 2           | 1045          | 1055          
gitcruz       | Fernando Cruz         | CNAG        | 13            | 2025-11-17  | Y      | 1           | 1025          | 1055          
andar27       | Adama Ndar            | Genoscope   | 7             | 2025-10-31  | Y      | 2           | 1044          | 1054          
ldemirdj      | Lola Demirdjian       | Genoscope   | 11            | 2025-10-14  | Y      | 2           | 1040          | 1050          
CaroB-M       | Caroline Menguy       | Genoscope   | 12            | 2025-11-13  | Y      | 2           | 1040          | 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          
auryjm        | Jean-Marc Aury        | Genoscope   | 12            | 2025-11-18  | Y      | 2           | 1039          | 1049          
EmilieTeo     | Emilie Teodori        | Genoscope   | 12            | 2025-11-21  | Y      | 2           | 1039          | 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: 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 (1067)

[erga-ear-bot]

Hi @DomAbsolon, do you agree to review this assembly?
Please reply to this message only with Yes or No by 02-Dec-2025 at 13:55 CET

[erga-ear-bot]

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

[erga-ear-bot]

*****
EAR Reviewer Selection Process
Date: 2025-12-02 21:20

All Eligible Candidates:

Github ID     | Full Name             | Institution | Total Reviews | Last Review | Active | Working PRs | Calling Score | Adjusted Score
-----------------------------------------------------------------------------------------------------------------------------------------
ldemirdj      | Lola Demirdjian       | Genoscope   | 11            | 2025-10-14  | Y      | 1           | 1041          | 1071          
CaroB-M       | Caroline Menguy       | Genoscope   | 14            | 2025-12-02  | Y      | 1           | 1039          | 1069          
bistace       | Benjamin Istace       | Genoscope   | 8             | 2025-12-01  | Y      | 2           | 1045          | 1055          
gitcruz       | Fernando Cruz         | CNAG        | 13            | 2025-11-17  | Y      | 1           | 1025          | 1055          
auryjm        | Jean-Marc Aury        | Genoscope   | 12            | 2025-11-18  | Y      | 2           | 1040          | 1050          
EmilieTeo     | Emilie Teodori        | Genoscope   | 12            | 2025-11-21  | Y      | 2           | 1040          | 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: Lola Demirdjian (ldemirdj)
The decision was based on:
- different institution ('Genoscope')
- active ('Y')
- working on 1 PR(s) currently
- highest adjusted calling score in this particular selection (1071)
  (Note: Adjusted score already considering -20 points due to 1 ongoing PR(s))

[erga-ear-bot]

Hi @ldemirdj, do you agree to review this assembly?
Please reply to this message only with Yes or No by 09-Dec-2025 at 02:19 CET

[ldemirdj]

Hi @Estel-Kitsune,

Congratulations on the assembly! I’ve just finished the first round of review. I have quite a few comments, so I’ll go chromosome by chromosome.

First, I would have tagged scaffolds 24, 16, and 13 as contaminants, as they show weak linkage and a noticeable drop in coverage.

Chromosome 1:
From 0 to 575.11 kbp, this region appears to be a haplotig, which is also evident when comparing with the region at 19.18 Mbp.

Chromosome 3:
I would have placed scaffold 44 into the gap at 55.29 Mbp.

Chromosome 6:
I would have assigned scaffold 23 as unloc for this chromosome.

Chromosome 7:
There is an inversion from the start up to 8.60 Mbp (with a gap present). I would also have moved scaffold 18 to the beginning, although I’m not fully sure about its orientation. Finally, scaffolds 70 and 73 should also be marked as unloc for this chromosome.

Chromosome 11:
The presence of a telomere suggests an inversion at the beginning, up to 12.10 Mbp.

Chromosome 12:
I would have placed scaffold 30 into the gap at 1.15 Mbp. I would have also marked scaffold 51 as unloc.

Chromosome 13:
Scaffolds 31, 9, and 2 should also be unloc.

Chromosome 16:
Scaffold 11 should be placed at the beginning of the chromosome.

Thanks, let me know if you need anything! Looking forward for the new map.

Lola

[erga-ear-bot]

Invalid confirmation!
Hi @ldemirdj, do you agree to review this assembly?
Please reply to this message only with Yes or No by 10-Dec-2025 at 20:36 CET

[ldemirdj]

Yes

[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.

[erga-ear-bot]

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

[tbrown91]

Hi @ldemirdj have you had a chance to have a look at this assembly?

[ldemirdj]

Hi @tbrown91, Yes, I already posted my comments above. :)

[tbrown91]

ah sorry, I only scrolled as far as the bot 🤦

@Estel-Kitsune can you have a look through and hopefully we can get this assembly through fairly quickly

[Estel-Kitsune]

Hi @ldemirdj, thank you for reviewing my 1st BGE assembly! I will incorporate your suggestions in my assembly.

Regarding scaffolds 24, 16, and 13 (the contaminants), should I just remove them from the assembly, or tag them as contaminant in PretextView?

[tbrown91]

Hi @Estel-Kitsune please just remove them and then regenerate the map. Great job!

[erga-ear-bot]

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

[erga-ear-bot]

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

[erga-ear-bot]

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