sPriGla3_EAR by diegomics · Pull Request #399 · ERGA-consortium/EARs

diegomics · 2026-06-15T16:14:04Z

Assembly review request

ToLID: sPriGla3
Species: Prionace glauca
Project: ERGA-Community
Affiliation: IZW

erga-ear-bot · 2026-06-15T16:14:48Z

Hi @diegomics, thanks for sending the EAR of Prionace glauca.
I added the corresponding tag to the PR and will contact a supervisor and a reviewer ASAP.

erga-ear-bot · 2026-06-15T16:14:51Z

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

diegomics · 2026-06-15T16:16:07Z

We supported @Sofia-Alves-Gen with the assembly of the genome using Galaxy, and later took over curation. @henryspaul was the main curator while Thieres collaborated. The guys are learning and think that a fresh pair of eyes would be helpful. The idea is to try to remove chaff with purge dups once things are more or less settled with the manual curation. Please see the provisional curator notes that @henryspaul prepared here with d-genies plots and more stuff: https://hackmd.io/@rh6i_ZNfTT6VuZZJCPxKBQ/rkeqMrIlMl

additive3 · 2026-06-16T08:52:22Z

OK

erga-ear-bot · 2026-06-16T08:53:23Z

*****
EAR Reviewer Selection Process
Date: 2026-06-16 08:53

All Eligible Candidates:

Github ID     | Full Name             | Institution | Total Reviews | Last Review | Active | Working PRs | Calling Score | Adjusted Score
-----------------------------------------------------------------------------------------------------------------------------------------
EmilieTeo     | Emilie Teodori        | Genoscope   | 21            | 2026-06-05  | Y      | 0           | 1040          | 1040          
gbdias        | Guilherme Dias        | SciLifeLab  | 9             | 2026-04-23  | Y      | 0           | 1027          | 1027          
additive3     | Jo Wood               | Sanger      | 10            | 2026-02-27  | Y      | 0           | 1030          | 1025          
bistace       | Benjamin Istace       | Genoscope   | 17            | 2026-04-22  | Y      | 1           | 1045          | 1025          
auryjm        | Jean-Marc Aury        | Genoscope   | 17            | 2026-06-09  | Y      | 1           | 1044          | 1024          
gitcruz       | Fernando Cruz         | CNAG        | 17            | 2026-06-05  | Y      | 1           | 1042          | 1022          
jesgomez      | Jessica Gomez Garrido | CNAG        | 19            | 2026-04-22  | Y      | 1           | 1039          | 1019          
tommathers    | Tom Mathers           | Sanger      | 8             | 2026-02-20  | Y      | 1           | 1032          | 1012          
DomAbsolon    | Dom Absolon           | Sanger      | 9             | 2026-03-12  | Y      | 1           | 1031          | 1011          
SarahPelan    | Sarah Pelan           | Sanger      | 9             | 2026-04-09  | Y      | 1           | 1031          | 1011          
MartinPippel  | Martin Pippel         | SciLifeLab  | 6             | 2026-05-18  | Y      | 1           | 1030          | 1010          
msozzoni      | Marcella Sozzoni      | UNIFI       | 3             | 2026-02-19  | Y      | 0           | 1007          | 1007          
talioto       | Tyler Alioto          | CNAG        | 10            | 2026-02-20  | Y      | 2           | 1047          | 1007          
joannacollins | Jo Collins            | Sanger      | 8             | 2026-02-24  | Y      | 2           | 1032          | 992           

Selected reviewer: Emilie Teodori (EmilieTeo)
The decision was based on:
- different institution ('Genoscope')
- active ('Y')
- working on 0 PR(s) currently
- highest adjusted calling score in this particular selection (1040)

erga-ear-bot · 2026-06-16T08:53:25Z

Hi @EmilieTeo, do you agree to review this assembly?
Please reply to this message only with Yes or No by 22-Jun-2026 at 14:53 CET

EmilieTeo · 2026-06-16T09:04:01Z

No

erga-ear-bot · 2026-06-16T09:05:07Z

@EmilieTeo Ok thank you, I will look for the next reviewer on the list :)

erga-ear-bot · 2026-06-16T09:05:08Z

*****
EAR Reviewer Selection Process
Date: 2026-06-16 09:05

All Eligible Candidates:

Github ID     | Full Name             | Institution | Total Reviews | Last Review | Active | Working PRs | Calling Score | Adjusted Score
-----------------------------------------------------------------------------------------------------------------------------------------
gbdias        | Guilherme Dias        | SciLifeLab  | 9             | 2026-04-23  | Y      | 0           | 1027          | 1027          
additive3     | Jo Wood               | Sanger      | 10            | 2026-02-27  | Y      | 0           | 1030          | 1025          
bistace       | Benjamin Istace       | Genoscope   | 17            | 2026-04-22  | Y      | 1           | 1045          | 1025          
auryjm        | Jean-Marc Aury        | Genoscope   | 17            | 2026-06-09  | Y      | 1           | 1044          | 1024          
gitcruz       | Fernando Cruz         | CNAG        | 17            | 2026-06-05  | Y      | 1           | 1042          | 1022          
EmilieTeo     | Emilie Teodori        | Genoscope   | 21            | 2026-06-05  | Y      | 1           | 1040          | 1020          
jesgomez      | Jessica Gomez Garrido | CNAG        | 19            | 2026-04-22  | Y      | 1           | 1039          | 1019          
tommathers    | Tom Mathers           | Sanger      | 8             | 2026-02-20  | Y      | 1           | 1032          | 1012          
DomAbsolon    | Dom Absolon           | Sanger      | 9             | 2026-03-12  | Y      | 1           | 1031          | 1011          
SarahPelan    | Sarah Pelan           | Sanger      | 9             | 2026-04-09  | Y      | 1           | 1031          | 1011          
MartinPippel  | Martin Pippel         | SciLifeLab  | 6             | 2026-05-18  | Y      | 1           | 1030          | 1010          
msozzoni      | Marcella Sozzoni      | UNIFI       | 3             | 2026-02-19  | Y      | 0           | 1007          | 1007          
talioto       | Tyler Alioto          | CNAG        | 10            | 2026-02-20  | Y      | 2           | 1047          | 1007          
joannacollins | Jo Collins            | Sanger      | 8             | 2026-02-24  | Y      | 2           | 1032          | 992           

Selected reviewer: Guilherme Dias (gbdias)
The decision was based on:
- different institution ('SciLifeLab')
- active ('Y')
- working on 0 PR(s) currently
- highest adjusted calling score in this particular selection (1027)

erga-ear-bot · 2026-06-16T09:05:10Z

Hi @gbdias, do you agree to review this assembly?
Please reply to this message only with Yes or No by 22-Jun-2026 at 15:04 CET

erga-ear-bot · 2026-06-22T14:39:20Z

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

erga-ear-bot · 2026-06-22T14:39:22Z

*****
EAR Reviewer Selection Process
Date: 2026-06-22 14:39

All Eligible Candidates:

Github ID     | Full Name             | Institution | Total Reviews | Last Review | Active | Working PRs | Calling Score | Adjusted Score
-----------------------------------------------------------------------------------------------------------------------------------------
additive3     | Jo Wood               | Sanger      | 10            | 2026-02-27  | Y      | 0           | 1030          | 1025          
bistace       | Benjamin Istace       | Genoscope   | 17            | 2026-04-22  | Y      | 1           | 1045          | 1025          
auryjm        | Jean-Marc Aury        | Genoscope   | 17            | 2026-06-09  | Y      | 1           | 1044          | 1024          
gitcruz       | Fernando Cruz         | CNAG        | 17            | 2026-06-05  | Y      | 1           | 1042          | 1022          
EmilieTeo     | Emilie Teodori        | Genoscope   | 21            | 2026-06-05  | Y      | 1           | 1040          | 1020          
jesgomez      | Jessica Gomez Garrido | CNAG        | 19            | 2026-04-22  | Y      | 1           | 1039          | 1019          
tommathers    | Tom Mathers           | Sanger      | 8             | 2026-02-20  | Y      | 1           | 1032          | 1012          
DomAbsolon    | Dom Absolon           | Sanger      | 9             | 2026-03-12  | Y      | 1           | 1031          | 1011          
SarahPelan    | Sarah Pelan           | Sanger      | 9             | 2026-04-09  | Y      | 1           | 1031          | 1011          
MartinPippel  | Martin Pippel         | SciLifeLab  | 6             | 2026-05-18  | Y      | 1           | 1030          | 1010          
msozzoni      | Marcella Sozzoni      | UNIFI       | 3             | 2026-02-19  | Y      | 0           | 1007          | 1007          
gbdias        | Guilherme Dias        | SciLifeLab  | 9             | 2026-04-23  | Y      | 1           | 1027          | 1007          
talioto       | Tyler Alioto          | CNAG        | 10            | 2026-02-20  | Y      | 2           | 1047          | 1007          
joannacollins | Jo Collins            | Sanger      | 8             | 2026-02-24  | Y      | 2           | 1032          | 992           

Selected reviewer: Jo Wood (additive3)
The decision was based on:
- different institution ('Sanger')
- active ('Y')
- working on 0 PR(s) currently
- oldest review and fewest reviews among the finalists (1025)

erga-ear-bot · 2026-06-22T14:39:24Z

Hi @additive3, do you agree to review this assembly?
Please reply to this message only with Yes or No by 26-Jun-2026 at 20:38 CET

additive3 · 2026-06-22T14:51:38Z

no

erga-ear-bot · 2026-06-22T14:53:04Z

@additive3 Ok thank you, I will look for the next reviewer on the list :)

erga-ear-bot · 2026-06-22T14:53:06Z

*****
EAR Reviewer Selection Process
Date: 2026-06-22 14:53

All Eligible Candidates:

Github ID     | Full Name             | Institution | Total Reviews | Last Review | Active | Working PRs | Calling Score | Adjusted Score
-----------------------------------------------------------------------------------------------------------------------------------------
bistace       | Benjamin Istace       | Genoscope   | 17            | 2026-04-22  | Y      | 1           | 1045          | 1025          
auryjm        | Jean-Marc Aury        | Genoscope   | 17            | 2026-06-09  | Y      | 1           | 1044          | 1024          
gitcruz       | Fernando Cruz         | CNAG        | 17            | 2026-06-05  | Y      | 1           | 1042          | 1022          
EmilieTeo     | Emilie Teodori        | Genoscope   | 21            | 2026-06-05  | Y      | 1           | 1040          | 1020          
jesgomez      | Jessica Gomez Garrido | CNAG        | 19            | 2026-04-22  | Y      | 1           | 1039          | 1019          
tommathers    | Tom Mathers           | Sanger      | 8             | 2026-02-20  | Y      | 1           | 1032          | 1012          
DomAbsolon    | Dom Absolon           | Sanger      | 9             | 2026-03-12  | Y      | 1           | 1031          | 1011          
SarahPelan    | Sarah Pelan           | Sanger      | 9             | 2026-04-09  | Y      | 1           | 1031          | 1011          
MartinPippel  | Martin Pippel         | SciLifeLab  | 6             | 2026-05-18  | Y      | 1           | 1030          | 1010          
msozzoni      | Marcella Sozzoni      | UNIFI       | 3             | 2026-02-19  | Y      | 0           | 1007          | 1007          
gbdias        | Guilherme Dias        | SciLifeLab  | 9             | 2026-04-23  | Y      | 1           | 1027          | 1007          
talioto       | Tyler Alioto          | CNAG        | 10            | 2026-02-20  | Y      | 2           | 1047          | 1007          
additive3     | Jo Wood               | Sanger      | 10            | 2026-02-27  | Y      | 1           | 1030          | 1005          
joannacollins | Jo Collins            | Sanger      | 8             | 2026-02-24  | Y      | 2           | 1032          | 992           

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 (1025)
  (Note: Adjusted score already considering -20 points due to 1 ongoing PR(s))

erga-ear-bot · 2026-06-22T14:53:07Z

Hi @bistace, do you agree to review this assembly?
Please reply to this message only with Yes or No by 26-Jun-2026 at 20:52 CET

bistace · 2026-06-23T07:05:18Z

No

erga-ear-bot · 2026-06-23T07:06:37Z

@bistace Ok thank you, I will look for the next reviewer on the list :)

erga-ear-bot · 2026-06-23T07:06:38Z

*****
EAR Reviewer Selection Process
Date: 2026-06-23 07:06

All Eligible Candidates:

Github ID     | Full Name             | Institution | Total Reviews | Last Review | Active | Working PRs | Calling Score | Adjusted Score
-----------------------------------------------------------------------------------------------------------------------------------------
auryjm        | Jean-Marc Aury        | Genoscope   | 17            | 2026-06-09  | Y      | 1           | 1044          | 1024          
gitcruz       | Fernando Cruz         | CNAG        | 17            | 2026-06-05  | Y      | 1           | 1042          | 1022          
EmilieTeo     | Emilie Teodori        | Genoscope   | 21            | 2026-06-05  | Y      | 1           | 1040          | 1020          
jesgomez      | Jessica Gomez Garrido | CNAG        | 19            | 2026-04-22  | Y      | 1           | 1039          | 1019          
tommathers    | Tom Mathers           | Sanger      | 8             | 2026-02-20  | Y      | 1           | 1032          | 1012          
DomAbsolon    | Dom Absolon           | Sanger      | 9             | 2026-03-12  | Y      | 1           | 1031          | 1011          
SarahPelan    | Sarah Pelan           | Sanger      | 9             | 2026-04-09  | Y      | 1           | 1031          | 1011          
MartinPippel  | Martin Pippel         | SciLifeLab  | 6             | 2026-05-18  | Y      | 1           | 1030          | 1010          
msozzoni      | Marcella Sozzoni      | UNIFI       | 3             | 2026-02-19  | Y      | 0           | 1007          | 1007          
gbdias        | Guilherme Dias        | SciLifeLab  | 9             | 2026-04-23  | Y      | 1           | 1027          | 1007          
talioto       | Tyler Alioto          | CNAG        | 10            | 2026-02-20  | Y      | 2           | 1047          | 1007          
additive3     | Jo Wood               | Sanger      | 10            | 2026-02-27  | Y      | 1           | 1030          | 1005          
bistace       | Benjamin Istace       | Genoscope   | 17            | 2026-04-22  | Y      | 2           | 1045          | 1005          
joannacollins | Jo Collins            | Sanger      | 8             | 2026-02-24  | Y      | 2           | 1032          | 992           

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 (1024)
  (Note: Adjusted score already considering -20 points due to 1 ongoing PR(s))

erga-ear-bot · 2026-06-23T07:06:40Z

Hi @auryjm, do you agree to review this assembly?
Please reply to this message only with Yes or No by 29-Jun-2026 at 13:06 CET

erga-ear-bot · 2026-06-29T13:06:37Z

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

erga-ear-bot · 2026-06-29T13:06:39Z

*****
EAR Reviewer Selection Process
Date: 2026-06-29 13:06

All Eligible Candidates:

Github ID     | Full Name             | Institution | Total Reviews | Last Review | Active | Working PRs | Calling Score | Adjusted Score
-----------------------------------------------------------------------------------------------------------------------------------------
gitcruz       | Fernando Cruz         | CNAG        | 17            | 2026-06-05  | Y      | 1           | 1042          | 1022          
EmilieTeo     | Emilie Teodori        | Genoscope   | 21            | 2026-06-05  | Y      | 1           | 1040          | 1020          
jesgomez      | Jessica Gomez Garrido | CNAG        | 19            | 2026-04-22  | Y      | 1           | 1039          | 1019          
tommathers    | Tom Mathers           | Sanger      | 8             | 2026-02-20  | Y      | 1           | 1032          | 1012          
DomAbsolon    | Dom Absolon           | Sanger      | 9             | 2026-03-12  | Y      | 1           | 1031          | 1011          
SarahPelan    | Sarah Pelan           | Sanger      | 9             | 2026-04-09  | Y      | 1           | 1031          | 1011          
MartinPippel  | Martin Pippel         | SciLifeLab  | 6             | 2026-05-18  | Y      | 1           | 1030          | 1010          
msozzoni      | Marcella Sozzoni      | UNIFI       | 3             | 2026-02-19  | Y      | 0           | 1007          | 1007          
gbdias        | Guilherme Dias        | SciLifeLab  | 9             | 2026-04-23  | Y      | 1           | 1027          | 1007          
talioto       | Tyler Alioto          | CNAG        | 10            | 2026-02-20  | Y      | 2           | 1047          | 1007          
additive3     | Jo Wood               | Sanger      | 10            | 2026-02-27  | Y      | 1           | 1030          | 1005          
bistace       | Benjamin Istace       | Genoscope   | 17            | 2026-04-22  | Y      | 2           | 1045          | 1005          
auryjm        | Jean-Marc Aury        | Genoscope   | 17            | 2026-06-09  | Y      | 2           | 1044          | 1004          
joannacollins | Jo Collins            | Sanger      | 8             | 2026-02-24  | Y      | 2           | 1032          | 992           

Selected reviewer: Fernando Cruz (gitcruz)
The decision was based on:
- different institution ('CNAG')
- active ('Y')
- working on 1 PR(s) currently
- highest adjusted calling score in this particular selection (1022)
  (Note: Adjusted score already considering -20 points due to 1 ongoing PR(s))

erga-ear-bot · 2026-06-29T13:06:40Z

Hi @gitcruz, do you agree to review this assembly?
Please reply to this message only with Yes or No by 03-Jul-2026 at 19:06 CET

erga-ear-bot · 2026-06-30T11:44:50Z

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

gitcruz · 2026-06-30T13:14:27Z

Yes

…

On Mon, 29 Jun 2026 at 15:07, erga-ear-bot[bot] ***@***.***> wrote: *erga-ear-bot[bot]* left a comment (ERGA-consortium/EARs#399) <#399 (comment)> Hi @gitcruz <https://github.com/gitcruz>, do you agree to review this assembly? Please reply to this message only with *Yes* or *No* by 03-Jul-2026 at 19:06 CET — Reply to this email directly, view it on GitHub <#399?email_source=notifications&email_token=AB34KVMNJOE2HTFEQU6AXVD5CJSXPA5CNFSNUABFM5UWIORPF5TWS5BNNB2WEL2JONZXKZKDN5WW2ZLOOQXTIOBTGI4TEOJRGE22M4TFMFZW63VHNVSW45DJN5XKKZLWMVXHJLDGN5XXIZLSL5RWY2LDNM#issuecomment-4832929115>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AB34KVL56YZHD2LS7A5TF7T5CJSXPAVCNFSNUABFKJSXA33TNF2G64TZHM3DCMZYG42TQMRUHNEXG43VMU5TINRWGY4DKMJZGMY2C5QC> . Triage notifications, keep track of coding agent tasks and review pull requests on the go with GitHub Mobile for iOS <https://github.com/notifications/mobile/ios/AB34KVPDGW5QDPT3VDUUPH35CJSXPA5CNFSNUABFM5UWIORPF5TWS5BNNB2WEL2JONZXKZKDN5WW2ZLOOQXTIOBTGI4TEOJRGE22M4TFMFZW63VHNVSW45DJN5XKKZLWMVXHJKTGN5XXIZLSL5UW64Y> and Android <https://github.com/notifications/mobile/android/AB34KVNAJI4Z5C7HEZ3SEOT5CJSXPA5CNFSNUABFM5UWIORPF5TWS5BNNB2WEL2JONZXKZKDN5WW2ZLOOQXTIOBTGI4TEOJRGE22M4TFMFZW63VHNVSW45DJN5XKKZLWMVXHJLTGN5XXIZLSL5QW4ZDSN5UWI>. Download it today! You are receiving this because you were mentioned.Message ID: ***@***.***>

erga-ear-bot · 2026-06-30T13:14:58Z

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.

gitcruz · 2026-07-01T10:08:17Z

Hi @diegomics,

Congratulations, this is an excellent diploid assembly. After reviewing the diploid contact map (by loading the provided .savestate) and reading the curator notes, I have produced a new savestate containing my review (BSH_AssemblyL1_Scaffolded_Hap1Hap2_tracks.pretext.savestate_FC_1).

Please find my comments below:

Karyotype 39 and missing autosome 38: The map contained 37 painted super-scaffolds plus the X chromosome (n=38). However, as you noted in the EAR, the map supports a karyotype of n=39. I consider HAP1_scaffold_38 and HAP2_scaffold_39 to correspond to an additional, separate autosome (autosome number 38). This region contains many repeats that are difficult to localize, order, and orient. Please see Scaffold_76 and Scaffold_77 in .savestate_FC_1 for reference.
Evolutionary Origin & Telomeres of X Chromosome: WGAs and synteny analysis suggest this chromosome likely originated from a fission of the ancestral X chromosome (e.g., Carcharhinus amblyrhynchos), or that a fusion involving the X chromosome occurred in at least two species (M. asterias and C. amblyrhynchos). While the distribution of telomere motifs could clarify this, the provided map unfortunately lacks information in the telomere extension. That said, analyzing the telomere distribution within the X chromosome of these other species could reveal if it was the product of a fusion (indicated by internal telomere peaks).
Micro-chromosomes and Chaff: Regarding the karyotype of n=43 reported by Asahida et al., 1995, is possible that the missing 4 chromosomes correspond with some of the small micro-chromosomes, that are likely highly heterochromatic and repetitive. I also noticed that 2n=86 was also found by BFC in another study (check the Animal Genome Size Database: https://www.genomesize.com/). For the sake of completeness, please make sure that most of the chaff is uploaded together with the representative haplotype (hap1).
Contaminants: Regarding the 45 contaminants detected by blobtoolkit in each haplotype: are you sure that all of them are false positive hits? Judging by the map, everything seems to be part of the same genome.
Haplotigs Painting (optional): Please note, that I realized that all the haplotigs were not painted together with their corresponding SUPER (1, 40,44,51,52,58…). While this may not be strictly necessary since they will be removed, I habitually paint them this way, which you can see in .savestate_FC_1.

As I said, this is a high-quality chromosome leve assembly of the blue shark genome. Please let me know your thoughts on these comments before we go ahead with the final approval.

Best regards,
Nando

diegomics · 2026-07-01T11:56:50Z

Thanks for the great review Nando, this feedback is very useful for @henryspaul
We will come back with a new version soon

gitcruz · 2026-07-01T14:15:53Z

Glad to help.

By the way @diegomics there's something in the EAR that's not right. The genome size retrieved is wrong, I checked goat and animal Genome Size Database and the expected should be 4.2 Gb: https://goat.genomehubs.org/Prionace_glauca Maybe is something to revise in the make_EAR.py code.

diegomics · 2026-07-01T15:12:32Z

The current EAR script is retrieving the estimated genome size from the provided Genomescope2. This (and many other things) should be improved with the new EAR script in a few weeks

erga-ear-bot · 2026-07-08T22:04:36Z

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

erga-ear-bot · 2026-07-16T10:59:36Z

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

erga-ear-bot · 2026-07-23T11:08:34Z

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

sPriGla3_EAR

6173cef

erga-ear-bot Bot added the ERGA-Community label Jun 15, 2026

erga-ear-bot Bot assigned additive3 Jun 16, 2026

erga-ear-bot Bot requested a review from gitcruz June 30, 2026 13:14

erga-ear-bot Bot added DELAYED STALLED labels Jul 29, 2026

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diegomics commented Jun 15, 2026

Assembly review request

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gitcruz commented Jun 30, 2026 via email

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gitcruz commented Jul 1, 2026 •

edited

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gitcruz commented Jul 1, 2026 •

edited

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