kaMicPoly1 EAR

[ilenia6]

Assembly review request

• ToLID: kaMicPoly1
• Species: Microcosmus polymorphus
• Project: ERGA-BGE
• Affiliation: UNIBA

[erga-ear-bot]

Hi @ilenia6, thanks for sending the EAR of Microcosmus polymorphus.
I added the corresponding tag to the PR and will contact a supervisor and a reviewer ASAP.

[erga-ear-bot]

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

[diegomics]

ok

[erga-ear-bot]

*****
EAR Reviewer Selection Process
Date: 2025-12-10 14:47

All Eligible Candidates:

Github ID     | Full Name             | Institution | Total Reviews | Last Review | Active | Working PRs | Calling Score | Adjusted Score
-----------------------------------------------------------------------------------------------------------------------------------------
bistace       | Benjamin Istace       | Genoscope   | 10            | 2025-12-10  | Y      | 1           | 1043          | 1073          
EmilieTeo     | Emilie Teodori        | Genoscope   | 14            | 2025-12-05  | Y      | 1           | 1038          | 1068          
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           | 1023          | 1053          
joannacollins | Jo Collins            | Sanger      | 6             | 2025-10-10  | Y      | 1           | 1023          | 1053          
tommathers    | Tom Mathers           | Sanger      | 7             | 2025-10-16  | Y      | 1           | 1022          | 1052          
gbdias        | Guilherme Dias        | SciLifeLab  | 4             | 2025-11-19  | Y      | 1           | 1021          | 1051          
DomAbsolon    | Dom Absolon           | Sanger      | 8             | 2025-11-04  | Y      | 1           | 1021          | 1051          
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          
CaroB-M       | Caroline Menguy       | Genoscope   | 14            | 2025-12-02  | Y      | 2           | 1039          | 1049          
additive3     | Jo Wood               | Sanger      | 8             | 2025-10-17  | Y      | 1           | 1021          | 1046          
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: Benjamin Istace (bistace)
The decision was based on:
- different institution ('Genoscope')
- active ('Y')
- working on 1 PR(s) currently
- highest adjusted calling score in this particular selection (1073)
  (Note: Adjusted score already considering -20 points due to 1 ongoing PR(s))

[erga-ear-bot]

Hi @bistace, do you agree to review this assembly?
Please reply to this message only with Yes or No by 16-Dec-2025 at 19:47 CET

[bistace]

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.

[bistace]

Hi @ilenia6,

congrats for this assembly as it looks clean. The telomeres are mostly where we expect them and I do not see large misassemblies. Here are a few things I did to the map:

• Super_1 at 24.6Mb and 28.2: haplotig
• Moved Super_1 at 33.15Mb to 33.22Mb
• Moved Super_1 from 43.4 Mb to the end to 42.9Mb (this puts the telomere signal at the wrong place but I think it looks better with the contacts)
• Inverted Super_3 from 5.6Mb to 6.3Mb
• The white cross in Super_3 at 17.7Mb seems to go with Super_4 as it shows lots of contacts but I did not find a way to place it in a gap
• Super_3 at 29.8Mb: haplotig
• Super_6 at 9.7Mb: haplotig
• Super_9 at 15.6Mb: haplotig
• I did not have the time to do it but you can tag a lot of small sequences as unlocs/haplotigs of the chromosomes (example: scaffold_62 and scaffold_98 with Super_12)

Here is my savestate.

[erga-ear-bot]

Attention @bistace, the EAR PDF was updated.

[ilenia6]

Hi @bistace , thank you for all your suggestions! I've updated the report, I had some problems loading your savestate so I implemented all the suggested modifications by myself. I've also moved some other unlocs and haplotigs. Let me know if it works now, and thank you again!

[bistace]

Hi @ilenia6 and thank you for making the changes. It seems that I cannot download the new pretext map as it is saying "You are not allowed to access this dataset", could you please check?

[ilenia6]

@bistace sorry, I changed the permissions, let me know if it works now

[bistace]

It's fine now, thank you!

[diegomics]

Just wondering, hifiasm didn't work for this assembly? The qv is quite low (sub EBP recommendation), yet you have a ton of data. Also, the gaps are quite high. Is the HiC data from the same individual?

[bistace]

After your edits the map seems fine to me but I found that a lot of unplaced sequences could be placed / put as unloc. I have uploaded the map and its savestate here so we can make sure that you can load it @ilenia6.

[erga-ear-bot]

Attention @bistace, the EAR PDF was updated.

[ilenia6]

Hi @bistace and thank you again for you help and feedback! I've been able now to load your savestate, and I also tried to place the unlocs. It looks fine to me now, let me know if you have any other suggestion.

[carmelagissi]

Just wondering, hifiasm didn't work for this assembly? The qv is quite low (sub EBP recommendation), yet you have a ton of data. Also, the gaps are quite high. Is the HiC data from the same individual?

Hi Diego. Yes, the HiC is from the same individual. Ilenia assembled directly with NECAT without trying using HiFiasm, also becasue when we obtained the long reads, the Hifiasm working with ONT reads was not yet available.

[erga-ear-bot]

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

[bistace]

Hi @ilenia6 and a happy new year to everyone!
The map looks fine to me so you can go ahead and regenerate the EAR and the map!