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Add Viola uliginosa #201

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@ldemirdj ldemirdj commented Aug 19, 2025 •
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Assembly review request

  • ToLID: ddVioUlig1
  • Species: Viola uliginosa
  • Project: ERGA-BGE
  • Affiliation: Genoscope

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erga-ear-bot bot commented Aug 19, 2025

Hi @ldemirdj, thanks for sending the EAR of Viola uliginosa.
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 Aug 19, 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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erga-ear-bot bot commented Aug 26, 2025

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

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diegomics commented Aug 28, 2025

Hi @additive3 do you want me to handle this one? Maybe you missed it :)

@erga-ear-bot erga-ear-bot bot added the ERROR! label Aug 28, 2025
@diegomics diegomics removed the ERROR! label Aug 28, 2025
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additive3 commented Aug 28, 2025

@diegomics Ha! I did completely miss this...
Happy to pick it up. Will give a response by end of day

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erga-ear-bot bot commented Aug 28, 2025

Invalid confirmation!

@erga-ear-bot erga-ear-bot bot added the ERROR! label Aug 28, 2025
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additive3 commented Aug 28, 2025 via email

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erga-ear-bot bot commented Aug 28, 2025 

*****
EAR Reviewer Selection Process
Date: 2025-08-28 13:50

All Eligible Candidates:

Github ID | Full Name      | Institution | Total Reviews | Last Review | Active | Busy | Calling Score | Adjusted Score
-----------------------------------------------------------------------------------------------------------------------
additive3 | Jo Wood        | Sanger      | 5             | 2025-02-27  | Y      | N    | 1015          | 1060          
tbrown91  | Tom Brown      | IZW         | 11            | 2025-07-29  | Y      | N    | 991           | 986           
diegomics | Diego De Panis | IZW         | 9             | 2025-03-25  | Y      | N    | 990           | 985           

Selected reviewer: Jo Wood (additive3)
The decision was based on:
- different institution ('Sanger')
- active ('Y')
- not busy ('N')
- highest adjusted calling score in this particular selection (1060)

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erga-ear-bot bot commented Aug 28, 2025

Hi @additive3, do you agree to review this assembly?
Please reply to this message only with Yes or No by 03-Sep-2025 at 19:50 CET

@diegomics diegomics removed the ERROR! label Aug 28, 2025
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diegomics commented Aug 28, 2025

Bot, behave! ;P
Please Jo, reply No so Tom can be the rev

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additive3 commented Aug 28, 2025 via email

@erga-ear-bot erga-ear-bot bot requested a review from additive3 August 28, 2025 14:05
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erga-ear-bot bot commented Aug 28, 2025

Thanks for agreeing!
I appointed you as the EAR reviewer.
I will keep your status as Busy 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.

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diegomics commented Aug 28, 2025

this thing is having a day... I'll fix it manually

@diegomics diegomics requested review from tbrown91 and removed request for additive3 August 28, 2025 14:07
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tbrown91 commented Aug 28, 2025

Hi @ldemirdj Overall this is looking really good. The ploidy of the species is perhaps making it difficult to tell what is a haplotig and what is a genuine part of the "primary" assembly.

I have few suggestions, see what you think:

Haplotig: 3:41.78-41.97Mb
3: unloc_2 -> unloc_1 @ 41.7Mb - both reverse orientation. Invert 3:36.45-41.7Mb
4: unloc_2 @ 6.1Mb
5: I'm not sure if most of these unlocs are haplotigs. Maybe safest to leave them as is

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ldemirdj commented Aug 29, 2025

Hi @tbrown91, I will take a look at your suggestions. Thanks!

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additive3 commented Aug 29, 2025

Hi @ldemirdj

I'd suggest the following updates.
1: unloc_1 (+ve) localses to 33.67Mb
3: What Tom says
4: unloc_2 is haptig - many of the other small unloc contigs are also haptigs
6: 15.53-24.08Mb invert
7, 9, 10: somthing odd happening with these chromosomes. looks like lot of translocaitions happening and missing sequence likely in the other assembly...this shows in the kmer spectra, I would suggest curating both side by side.

Do you have the genomescope profile and combined mequry spectra for combined pri/alt?

Other observations...
high busco duplication b/c there is visible ancient genome duplication. amazed it is so high

Where did the "Expected size" come from as 1C (Kew) and 2C/4C (tetraploidy has been reported) Slazak et al. 2014 are consistent with the haploid gneome being ~670Mb

I note there are tracks for mito/chloro - these seem to indicate a large proportion of the remaining small contig are organelle... is that the case or am I missing something... if so these should be removed.

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ldemirdj commented Sep 4, 2025

Hi,

Thank you for your detailed feedback.

I have made the suggested modifications, as I fully agree with your comments. However, I am not sure I fully understand the point regarding chromosome 3 — could you clarify what exactly you meant there?

As requested, I’m attaching the GenomeScope profile and the KAT spectra graph.

Regarding the “Expected size” reported in the EAR, I am not sure where that figure comes from either. From what I know, they usually take the size from GOAT.

For the mitochondrial and chloroplast contigs, I’ll take care of that.

Best regards,

Lola

téléchargement (1) téléchargement

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tbrown91 commented Sep 4, 2025

I think I created an extra unloc sequence for scaffold 3 in my mind.

there is a duplication in scaffold 3 from 41.78-41.97Mb

The unloc looks like it belongs here and the sequence beforehand from 36.45Mb-41.7Mb looks like it should be inverted

image

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ldemirdj commented Sep 4, 2025

Okay, thanks @tbrown91 :)

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erga-ear-bot bot commented Sep 24, 2025

Attention @tbrown91, the EAR PDF was updated.

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erga-ear-bot bot commented Oct 1, 2025

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

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erga-ear-bot bot commented Oct 9, 2025

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

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additive3 commented Oct 9, 2025

Hi @ldemirdj

Did you get anywhere with producing and looking at the diploid assembly side by side?

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ldemirdj commented Oct 10, 2025 •
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Hi @additive3,

Thanks for your message. I’ve already updated the EAR a few weeks ago, incorporating both Tom’s comments and the modifications you suggested. I also addressed your previous questions and uploaded the revised version online.

Could you please confirm if you’re referring to something specific that still needs to be compared or added regarding the assembly?

Best,

@additive3
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additive3 commented Oct 10, 2025

HI @ldemirdj

I raised a query surrounding chrm scaffolds 7, 9, 10 (see below):
7, 9, 10: somthing odd happening with these chromosomes. looks like lot of translocaitions happening and missing sequence likely in the other assembly...this shows in the kmer spectra, I would suggest curating both side by side.

Adding in images to show you the issues.
Screenshot 2025-10-10 at 11 34 35
Screenshot 2025-10-10 at 11 35 23
Screenshot 2025-10-10 at 11 35 44

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ldemirdj commented Oct 10, 2025 •
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Hi @additive3,

Thanks for your message and for pointing this out. I took a closer look at chromosomes 7, 9, and 10 as you suggested. You were absolutely right — I had misunderstood the situation initially. The translocations and missing sequences you mentioned do seem to indicate assembly discrepancies.

However, curating both assemblies side by side would take quite a lot of time, as I’d need to start the process from scratch. I’ll discuss this with our team to decide on the best way forward.

Best,

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additive3 commented Oct 10, 2025

Ok, no problem @ldemirdj .
Let me know how this goes.
I'm always available to provide support.

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erga-ear-bot bot commented Oct 17, 2025

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

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erga-ear-bot bot commented Oct 25, 2025

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

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erga-ear-bot bot commented Nov 1, 2025

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

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erga-ear-bot bot commented Nov 8, 2025

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

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erga-ear-bot bot commented Nov 16, 2025

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

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erga-ear-bot bot commented Nov 23, 2025

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

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diegomics commented Nov 26, 2025

Hi @ldemirdj, just checking if the PR is still alive... I'm going through all the EARs today! :P

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ldemirdj commented Nov 26, 2025

Hello @diegomics, yes, it's still in progress. It's taking me quite a while because I'm processing a lot of genomes at the same time. I'll keep you updated when it's finished. Thank you!

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erga-ear-bot bot commented Dec 3, 2025

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

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erga-ear-bot bot commented Dec 10, 2025

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

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erga-ear-bot bot commented Dec 16, 2025

Attention @ldemirdj, 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 Dec 16, 2025
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erga-ear-bot bot commented Dec 16, 2025

Attention @tbrown91, the EAR PDF was updated.

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erga-ear-bot bot commented Dec 16, 2025

Attention @tbrown91, the EAR PDF was updated.

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tbrown91 commented Dec 16, 2025

Hi @ldemirdj is there any chance that some of your unlocs have been included in the scaffolds? For example at the ends of scaffolds 2 & 3?

image

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tbrown91 commented Dec 16, 2025

I hope I'm looking at the correct map

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ldemirdj commented Dec 16, 2025

No, that's the wrong map, let me check :)

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