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Add_qqChaOliv1.1#339

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jesgomez wants to merge 2 commits intoERGA-consortium:mainfrom
jesgomez:qqChaOliv
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Add_qqChaOliv1.1#339
jesgomez wants to merge 2 commits intoERGA-consortium:mainfrom
jesgomez:qqChaOliv

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@jesgomez
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@jesgomez jesgomez commented Jan 28, 2026

Assembly review request

  • ToLID: qqChaOliv1
  • Species: Chaetopelma olivaceum
  • Project: ERGA-BGE
  • Affiliation: CNAG

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erga-ear-bot bot commented Jan 28, 2026

Hi @jesgomez, thanks for sending the EAR of Chaetopelma olivaceum.
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 Jan 28, 2026

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 Jan 28, 2026 via email

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erga-ear-bot bot commented Jan 28, 2026 

*****
EAR Reviewer Selection Process
Date: 2026-01-28 09:59

All Eligible Candidates:

Github ID     | Full Name        | Institution | Total Reviews | Last Review | Active | Working PRs | Calling Score | Adjusted Score
------------------------------------------------------------------------------------------------------------------------------------
auryjm        | Jean-Marc Aury   | Genoscope   | 14            | 2026-01-27  | Y      | 1           | 1041          | 1071          
MartinPippel  | Martin Pippel    | SciLifeLab  | 3             | 2026-01-20  | Y      | 1           | 1027          | 1057          
tommathers    | Tom Mathers      | Sanger      | 7             | 2025-10-16  | Y      | 1           | 1026          | 1056          
joannacollins | Jo Collins       | Sanger      | 7             | 2026-01-16  | Y      | 1           | 1026          | 1056          
DomAbsolon    | Dom Absolon      | Sanger      | 8             | 2025-11-04  | Y      | 1           | 1025          | 1055          
gbdias        | Guilherme Dias   | SciLifeLab  | 6             | 2026-01-23  | Y      | 1           | 1024          | 1054          
bistace       | Benjamin Istace  | Genoscope   | 12            | 2026-01-21  | Y      | 2           | 1044          | 1054          
ldemirdj      | Lola Demirdjian  | Genoscope   | 13            | 2026-01-27  | Y      | 2           | 1042          | 1052          
additive3     | Jo Wood          | Sanger      | 8             | 2025-10-17  | Y      | 1           | 1025          | 1050          
EmilieTeo     | Emilie Teodori   | Genoscope   | 15            | 2025-12-15  | Y      | 2           | 1040          | 1050          
CaroB-M       | Caroline Menguy  | Genoscope   | 17            | 2026-01-20  | Y      | 2           | 1039          | 1049          
msozzoni      | Marcella Sozzoni | UNIFI       | 0             | NA          | Y      | 3           | 1006          | 1046          
tbrown91      | Tom Brown        | IZW         | 12            | 2026-01-22  | Y      | 0           | 995           | 1040          
diegomics     | Diego De Panis   | IZW         | 11            | 2025-09-22  | Y      | 0           | 993           | 1038          
SarahPelan    | Sarah Pelan      | Sanger      | 7             | 2025-12-19  | Y      | 2           | 1026          | 1036          

Selected reviewer: Jean-Marc Aury (auryjm)
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))

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erga-ear-bot bot commented Jan 28, 2026

Hi @auryjm, do you agree to review this assembly?
Please reply to this message only with Yes or No by 03-Feb-2026 at 14:59 CET

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additive3 commented Jan 28, 2026

Hi @jesgomez

Nicely produced spider genome assembly.
Its a shame SUPER_7 is so fregmented. I had a play around with it but there are so many ambiguities I think it is correct to leave the majority as unlocalised.

Only query I have releates to the mapped read coverage. how have you mapped to the assembly as autosomes are showing double coverage to the sex chromosomes. Were they mapped to each assembly separately and merged?

Happy to sign off on the assembly otherwise

@jesgomez
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jesgomez commented Jan 28, 2026

thanks @additive3. To produce the coverage track the ont reads were aligned to the diploid fasta file with minimap2. Since we are not filtering out multimappings and there's only one copy of each X chromosome per 2 of each autosome, we get half cpverage.

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auryjm commented Jan 28, 2026

Yes

@erga-ear-bot erga-ear-bot bot requested a review from auryjm January 28, 2026 14:39
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erga-ear-bot bot commented Jan 28, 2026

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.

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additive3 commented Jan 28, 2026

@jesgomez

the ont reads were aligned to the diploid fasta file with minimap2

But that is not what are shown in the data...
if you mapped to the diploid genome then all the chromsomes should show the same coverage. but autosomes are 60X and sex chromosomes are 30X.. see image

Could this be pooled sample...(male and female)? probably not seeing as this is a tarantula species....

Screenshot 2026-01-28 at 15 17 29

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jesgomez commented Jan 28, 2026

well, that's what you would expect if we were only considering primary alignments, but since we don't filter out secondary alignments, we are like artificially "doubling" the coverage of the autosomes.

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auryjm commented Jan 28, 2026 •
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Hi @jesgomez,
Congratulations on this spider assembly. We generated another assembly from the same genus within BGE, but with a lower contig N50 (~10 Mb), although it is true that it was based on only ~20× PacBio data. I went through the Hi-C map and only identified a few unplaced sequences that could potentially be incorporated into chromosomes. However, I understand that this would require a substantial amount of work for a very small fraction of the assembly, so it is entirely up to you whether you want to place them and relaunch the workflow.

Specifically:

  • H2_scaffold_17 can be placed at the beginning of H2_SUPER_18
  • H1_scaffold_43 can be placed at the beginning of H1_SUPER_8
  • H2_scaffold_34 can be placed at the beginning of H2_SUPER_8
  • H2_scaffold_42 can be placed in forward orientation within the gap of H2_SUPER_16
  • H2_scaffold_37 can be placed at the beginning of H1_SUPER_2 (or left as unloc)
  • H1_scaffold_41 can be placed at the beginning of H2_SUPER_2 (or left as unloc)

In parallel, I suggest an organization for SUPER_7 based on the comparison of both haplotypes, which do not exhibit breakpoints at the same locations.

Here is my savestate :
qqChaOliv1.1.scrubbed.diploid_mq0.extensions.HR.pretext.zip

One last point regarding coverage: we also encountered an issue in another genome where secondary alignments were retained, which likely masked the expected half-coverage pattern of haplotigs (in the case of a haploid assembly/map).

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jesgomez commented Feb 5, 2026

Thanks @auryjm, I like your reorganization of SUPER_7 and most of your additional placements. I can produce the updated pdf for you to do a final check.

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erga-ear-bot bot commented Feb 12, 2026

Attention @auryjm, the EAR PDF was updated.

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auryjm commented Feb 13, 2026

Sounds good to me,
Congrats @jesgomez !

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erga-ear-bot bot commented Feb 13, 2026

Thanks @auryjm for the review.
I will add a new reviewed species for you to the table when @additive3 merges the PR ;)

Congrats on the assembly @jesgomez!
Please make sure that the fasta file to upload to ENA is generated based on the final reviewed version of the assembly.

After @additive3 confirmation, you can start with the assembly submission to save time.
The PR will be merged only when the final version of the EAR pdf is available.

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