Add ilHipCypr1_EAR #270

talioto · 2025-10-24T16:02:19Z

Assembly review request

ToLID: ilHipCypr1
Species: Hipparchia cypriensis
Project: ERGA-BGE
Affiliation: CNAG

erga-ear-bot · 2025-10-24T16:03:00Z

Hi @talioto, thanks for sending the EAR of Hipparchia cypriensis.
I added the corresponding tag to the PR and will contact a supervisor and a reviewer ASAP.

erga-ear-bot · 2025-10-24T16:03:03Z

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

talioto · 2025-10-24T16:05:34Z

made comment about not tagging the Z, but I did and it's the correct one. I can update the pdf.

diegomics · 2025-10-24T16:43:32Z

ok

erga-ear-bot · 2025-10-24T16:44:24Z

*****
EAR Reviewer Selection Process
Date: 2025-10-24 16:44

All Eligible Candidates:

Github ID     | Full Name       | Institution | Total Reviews | Last Review | Active | Working PRs | Calling Score | Adjusted Score
-----------------------------------------------------------------------------------------------------------------------------------
bistace       | Benjamin Istace | Genoscope   | 7             | 2025-10-17  | Y      | 1           | 1042          | 1072          
tommathers    | Tom Mathers     | Sanger      | 7             | 2025-10-16  | Y      | 0           | 1018          | 1068          
auryjm        | Jean-Marc Aury  | Genoscope   | 10            | 2025-10-20  | Y      | 1           | 1038          | 1068          
EmilieTeo     | Emilie Teodori  | Genoscope   | 10            | 2025-10-21  | Y      | 1           | 1038          | 1068          
CaroB-M       | Caroline Menguy | Genoscope   | 11            | 2025-10-20  | Y      | 1           | 1038          | 1068          
ldemirdj      | Lola Demirdjian | Genoscope   | 11            | 2025-10-14  | Y      | 1           | 1037          | 1067          
gbdias        | Guilherme Dias  | SciLifeLab  | 3             | 2025-10-23  | Y      | 0           | 1014          | 1064          
additive3     | Jo Wood         | Sanger      | 8             | 2025-10-17  | Y      | 0           | 1017          | 1062          
andar27       | Adama Ndar      | Genoscope   | 6             | 2025-10-17  | Y      | 2           | 1042          | 1052          
SarahPelan    | Sarah Pelan     | Sanger      | 6             | 2025-09-16  | Y      | 1           | 1019          | 1049          
joannacollins | Jo Collins      | Sanger      | 6             | 2025-10-10  | Y      | 1           | 1019          | 1049          
DomAbsolon    | Dom Absolon     | Sanger      | 7             | 2025-10-20  | Y      | 1           | 1018          | 1048          
MartinPippel  | Martin Pippel   | SciLifeLab  | 2             | 2025-10-06  | Y      | 1           | 1015          | 1045          
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: 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 (1072)
  (Note: Adjusted score already considering -20 points due to 1 ongoing PR(s))

erga-ear-bot · 2025-10-24T16:44:25Z

Hi @bistace, do you agree to review this assembly?
Please reply to this message only with Yes or No by 30-Oct-2025 at 22:44 CET

erga-ear-bot · 2025-10-30T21:17:08Z

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

erga-ear-bot · 2025-10-30T21:17:09Z

*****
EAR Reviewer Selection Process
Date: 2025-10-30 21:17

All Eligible Candidates:

Github ID     | Full Name       | Institution | Total Reviews | Last Review | Active | Working PRs | Calling Score | Adjusted Score
-----------------------------------------------------------------------------------------------------------------------------------
n-equals-one  | Tomas Larsson   | SciLifeLab  | 0             | NA          | Y      | 2           | 1017          | 1077          
EmilieTeo     | Emilie Teodori  | Genoscope   | 10            | 2025-10-21  | Y      | 1           | 1038          | 1068          
CaroB-M       | Caroline Menguy | Genoscope   | 11            | 2025-10-20  | Y      | 1           | 1038          | 1068          
ldemirdj      | Lola Demirdjian | Genoscope   | 11            | 2025-10-14  | Y      | 1           | 1037          | 1067          
gbdias        | Guilherme Dias  | SciLifeLab  | 3             | 2025-10-23  | Y      | 0           | 1014          | 1064          
andar27       | Adama Ndar      | Genoscope   | 6             | 2025-10-17  | Y      | 2           | 1042          | 1052          
bistace       | Benjamin Istace | Genoscope   | 7             | 2025-10-17  | Y      | 2           | 1042          | 1052          
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      | 7             | 2025-10-20  | Y      | 1           | 1018          | 1048          
auryjm        | Jean-Marc Aury  | Genoscope   | 10            | 2025-10-20  | Y      | 2           | 1038          | 1048          
MartinPippel  | Martin Pippel   | SciLifeLab  | 2             | 2025-10-06  | Y      | 1           | 1015          | 1045          
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: Tomas Larsson (n-equals-one)
The decision was based on:
- different institution ('SciLifeLab')
- active ('Y')
- working on 2 PR(s) currently
- highest adjusted calling score in this particular selection (1077)
  (Note: Adjusted score already considering -40 points due to 2 ongoing PR(s))

erga-ear-bot · 2025-10-30T21:17:11Z

Hi @n-equals-one, do you agree to review this assembly?
Please reply to this message only with Yes or No by 06-Nov-2025 at 02:16 CET

erga-ear-bot · 2025-11-06T09:22:00Z

@n-equals-one Time is out! I will look for the next reviewer on the list :)

erga-ear-bot · 2025-11-06T09:22:02Z

*****
EAR Reviewer Selection Process
Date: 2025-11-06 09:22

All Eligible Candidates:

Github ID     | Full Name       | Institution | Total Reviews | Last Review | Active | Working PRs | Calling Score | Adjusted Score
-----------------------------------------------------------------------------------------------------------------------------------
n-equals-one  | Tomas Larsson   | SciLifeLab  | 0             | NA          | Y      | 2           | 1019          | 1079          
EmilieTeo     | Emilie Teodori  | Genoscope   | 11            | 2025-11-05  | Y      | 1           | 1038          | 1068          
DomAbsolon    | Dom Absolon     | Sanger      | 8             | 2025-11-04  | Y      | 0           | 1017          | 1067          
bistace       | Benjamin Istace | Genoscope   | 7             | 2025-10-17  | Y      | 2           | 1043          | 1053          
andar27       | Adama Ndar      | Genoscope   | 7             | 2025-10-31  | Y      | 2           | 1042          | 1052          
SarahPelan    | Sarah Pelan     | Sanger      | 6             | 2025-09-16  | Y      | 1           | 1019          | 1049          
joannacollins | Jo Collins      | Sanger      | 6             | 2025-10-10  | Y      | 1           | 1019          | 1049          
CaroB-M       | Caroline Menguy | Genoscope   | 11            | 2025-10-20  | Y      | 2           | 1039          | 1049          
tommathers    | Tom Mathers     | Sanger      | 7             | 2025-10-16  | Y      | 1           | 1018          | 1048          
ldemirdj      | Lola Demirdjian | Genoscope   | 11            | 2025-10-14  | Y      | 2           | 1038          | 1048          
auryjm        | Jean-Marc Aury  | Genoscope   | 11            | 2025-11-04  | Y      | 2           | 1038          | 1048          
MartinPippel  | Martin Pippel   | SciLifeLab  | 2             | 2025-10-06  | Y      | 1           | 1017          | 1047          
gbdias        | Guilherme Dias  | SciLifeLab  | 3             | 2025-10-23  | Y      | 1           | 1016          | 1046          
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: Tomas Larsson (n-equals-one)
The decision was based on:
- different institution ('SciLifeLab')
- active ('Y')
- working on 2 PR(s) currently
- highest adjusted calling score in this particular selection (1079)
  (Note: Adjusted score already considering -40 points due to 2 ongoing PR(s))

erga-ear-bot · 2025-11-06T09:22:03Z

Hi @n-equals-one, do you agree to review this assembly?
Please reply to this message only with Yes or No by 12-Nov-2025 at 14:21 CET

erga-ear-bot · 2025-11-12T21:18:20Z

@n-equals-one Time is out! I will look for the next reviewer on the list :)

erga-ear-bot · 2025-11-12T21:18:22Z

*****
EAR Reviewer Selection Process
Date: 2025-11-12 21:18

All Eligible Candidates:

Github ID     | Full Name       | Institution | Total Reviews | Last Review | Active | Working PRs | Calling Score | Adjusted Score
-----------------------------------------------------------------------------------------------------------------------------------
tommathers    | Tom Mathers     | Sanger      | 7             | 2025-10-16  | Y      | 0           | 1018          | 1068          
DomAbsolon    | Dom Absolon     | Sanger      | 8             | 2025-11-04  | Y      | 0           | 1017          | 1067          
bistace       | Benjamin Istace | Genoscope   | 7             | 2025-10-17  | Y      | 2           | 1044          | 1054          
andar27       | Adama Ndar      | Genoscope   | 7             | 2025-10-31  | Y      | 2           | 1043          | 1053          
CaroB-M       | Caroline Menguy | Genoscope   | 11            | 2025-10-20  | 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          
ldemirdj      | Lola Demirdjian | Genoscope   | 11            | 2025-10-14  | Y      | 2           | 1039          | 1049          
auryjm        | Jean-Marc Aury  | Genoscope   | 11            | 2025-11-04  | Y      | 2           | 1039          | 1049          
EmilieTeo     | Emilie Teodori  | Genoscope   | 11            | 2025-11-05  | Y      | 2           | 1039          | 1049          
MartinPippel  | Martin Pippel   | SciLifeLab  | 2             | 2025-10-06  | Y      | 1           | 1017          | 1047          
gbdias        | Guilherme Dias  | SciLifeLab  | 3             | 2025-10-23  | Y      | 1           | 1016          | 1046          
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: Tom Mathers (tommathers)
The decision was based on:
- different institution ('Sanger')
- active ('Y')
- working on 0 PR(s) currently
- highest adjusted calling score in this particular selection (1068)

erga-ear-bot · 2025-11-12T21:18:23Z

Hi @tommathers, do you agree to review this assembly?
Please reply to this message only with Yes or No by 19-Nov-2025 at 02:17 CET

talioto · 2025-11-13T10:44:55Z

The EAR report says "post-curation" on the blobplot, but I provided the pre-curation blobplot to show the contaminants that were removed. I know it would be more work, but seeing the pre and post contamination plot together might be nice (if contamination is removed). @diegomics , can we make this flexible in the EAR? show pre, post or pre and post?

erga-ear-bot · 2025-11-19T09:22:05Z

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

erga-ear-bot · 2025-11-19T09:22:07Z

*****
EAR Reviewer Selection Process
Date: 2025-11-19 09:22

All Eligible Candidates:

Github ID     | Full Name       | Institution | Total Reviews | Last Review | Active | Working PRs | Calling Score | Adjusted Score
-----------------------------------------------------------------------------------------------------------------------------------
auryjm        | Jean-Marc Aury  | Genoscope   | 12            | 2025-11-18  | Y      | 1           | 1038          | 1068          
DomAbsolon    | Dom Absolon     | Sanger      | 8             | 2025-11-04  | Y      | 0           | 1017          | 1067          
bistace       | Benjamin Istace | Genoscope   | 7             | 2025-10-17  | Y      | 2           | 1044          | 1054          
andar27       | Adama Ndar      | Genoscope   | 7             | 2025-10-31  | Y      | 2           | 1043          | 1053          
MartinPippel  | Martin Pippel   | SciLifeLab  | 2             | 2025-10-06  | Y      | 1           | 1019          | 1049          
SarahPelan    | Sarah Pelan     | Sanger      | 6             | 2025-09-16  | Y      | 1           | 1019          | 1049          
joannacollins | Jo Collins      | Sanger      | 6             | 2025-10-10  | Y      | 1           | 1019          | 1049          
ldemirdj      | Lola Demirdjian | Genoscope   | 11            | 2025-10-14  | Y      | 2           | 1039          | 1049          
EmilieTeo     | Emilie Teodori  | Genoscope   | 11            | 2025-11-05  | Y      | 2           | 1039          | 1049          
CaroB-M       | Caroline Menguy | Genoscope   | 12            | 2025-11-13  | Y      | 2           | 1039          | 1049          
gbdias        | Guilherme Dias  | SciLifeLab  | 3             | 2025-10-23  | Y      | 1           | 1018          | 1048          
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: 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 (1068)
  (Note: Adjusted score already considering -20 points due to 1 ongoing PR(s))

erga-ear-bot · 2025-11-19T09:22:08Z

Hi @auryjm, do you agree to review this assembly?
Please reply to this message only with Yes or No by 25-Nov-2025 at 14:21 CET

auryjm · 2025-11-19T09:48:03Z

Yes

erga-ear-bot · 2025-11-19T09:49:23Z

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.

auryjm · 2025-11-19T18:29:28Z

Hi @talioto,

The assembly is of good quality with very few gaps!

I would just have assigned some small scaffolds in the shrapnel as contaminants. Here are my savestate and the list of scaffolds:
ilHipCypr1.hap1.cur.no_mt.scrubbed_mq0.extensions.HR.pretext.savestate_JMA.txt

Scaffold_55	1	23604	1	W	scaffold_86	1	23604	+	Contaminant
Scaffold_56	1	94418	1	W	scaffold_62	1	94418	+	Contaminant
Scaffold_57	1	41307	1	W	scaffold_75	1	41307	+	Contaminant
Scaffold_58	1	5901	1	W	scaffold_103	1	5901	+	Contaminant
Scaffold_59	1	17703	1	W	scaffold_98	1	17703	+	Contaminant
Scaffold_60	1	17703	1	W	scaffold_87	1	17703	+	Contaminant
Scaffold_61	1	5901	1	W	scaffold_106	1	5901	+	Contaminant
Scaffold_62	1	29505	1	W	scaffold_82	1	29505	+	Contaminant
Scaffold_63	1	17703	1	W	scaffold_97	1	17703	+	Contaminant
Scaffold_64	1	41307	1	W	scaffold_76	1	41307	+	Contaminant
Scaffold_65	1	17703	1	W	scaffold_91	1	17703	+	Contaminant
Scaffold_66	1	17703	1	W	scaffold_88	1	17703	+	Contaminant
Scaffold_67	1	11802	1	W	scaffold_105	1	11802	+	Contaminant
Scaffold_68	1	17703	1	W	scaffold_90	1	17703	+	Contaminant
Scaffold_69	1	23604	1	W	scaffold_85	1	23604	+	Contaminant
Scaffold_70	1	11802	1	W	scaffold_100	1	11802	+	Contaminant
Scaffold_71	1	17703	1	W	scaffold_96	1	17703	+	Contaminant
Scaffold_72	1	5901	1	W	scaffold_104	1	5901	+	Contaminant
Scaffold_73	1	106220	1	W	scaffold_58	1	106220	+	Contaminant
Scaffold_74	1	123923	1	W	scaffold_53	1	123923	+	Contaminant

talioto · 2025-11-20T12:25:38Z

out of curiosity, how did you identify the contaminants? Just by coverage? It's true, we could clean up the assembly by removing a lot of short, low coverage stuff. with telomeres on nearly every chr end and only a couple gaps, it's hard to see where these sequences would go - I asume most of it are error tips, bubbles etc from the assembly graph, not contamination. I don't have any problem removing them.

auryjm · 2025-11-20T15:46:18Z

Hi Tyler,

I tagged these scaffolds based first on their sparse Hi-C contacts with other sequences of the assembly, and second on their lower coverage.
At Genoscope, we also use (in addition to Context which is based on coverage, GC content, binning, gene prediction and taxonomic assignment) whokaryote and a search for known rRNAs. This gives us a list of candidates, which often strongly overlaps with the sequences highlighted from the Hi-C map.

talioto · 2025-11-20T17:11:34Z

OK, so I'll use your list and also apply a blobtools gc, length and ont coverage filter to remove some of the chaff. Otherwise, no other changes.

erga-ear-bot · 2025-11-27T21:17:54Z

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

erga-ear-bot · 2025-12-04T21:19:48Z

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

erga-ear-bot · 2025-12-11T21:25:30Z

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

talioto · 2025-12-19T13:58:35Z

I took a look at hap2 along with the curated (and decontaminated) hap1. the hap2 assembly is incomplete as hifiasm must have collapsed a few chromosomes. I think we'll submit the hap1 as primary and hap2 as alternate. I switched the assignment of one chromosome from hap2 to hap1 and vice versa in order to remove one of the two gaps from the assembly. here is the pretext and savestate.

auryjm · 2025-12-23T08:47:50Z

Hi @talioto,
As in the first round of review, I did not see many things that need to be changed. The contiguity is high and the assembly contains very few gaps.

I am not sure that hap1 was always selected as the longest haplotype. For example, between chr17 and chr18, hap2 is the longer one. It contains a region that appears to have been collapsed and assigned to hap2. Ideally, this region should be deduplicated, but this is not possible in Pretext. In any case, I suggest using chr18 as the hap1 version. The same applies to chr25 and chr26.

In addition, it seems that for some chromosomes the two haplotypes have been collapsed into a single sequence (chr31, chr40, chr41, chr46, and chr51), which suggests that they may also need to be included in hap2. The situation is a bit more complicated for chr36 and chr37, should they both have been tagged as hap1?

Add ilHipCypr1_EAR

8def6ad

erga-ear-bot bot added the ERGA-BGE label Oct 24, 2025

Fixed comment about Z.

a0f13c9

erga-ear-bot bot assigned diegomics Oct 24, 2025

erga-ear-bot bot requested a review from auryjm November 19, 2025 09:49

erga-ear-bot bot added DELAYED STALLED labels Dec 18, 2025

erga-ear-bot bot removed the STALLED label Dec 19, 2025

Add ilHipCypr1_EAR #270

Are you sure you want to change the base?

Add ilHipCypr1_EAR #270

Uh oh!

Conversation

talioto commented Oct 24, 2025

Assembly review request

Uh oh!

erga-ear-bot bot commented Oct 24, 2025

Uh oh!

erga-ear-bot bot commented Oct 24, 2025

Uh oh!

talioto commented Oct 24, 2025

Uh oh!

diegomics commented Oct 24, 2025

Uh oh!

erga-ear-bot bot commented Oct 24, 2025

Uh oh!

erga-ear-bot bot commented Oct 24, 2025

Uh oh!

erga-ear-bot bot commented Oct 30, 2025

Uh oh!

erga-ear-bot bot commented Oct 30, 2025

Uh oh!

erga-ear-bot bot commented Oct 30, 2025

Uh oh!

erga-ear-bot bot commented Nov 6, 2025

Uh oh!

erga-ear-bot bot commented Nov 6, 2025

Uh oh!

erga-ear-bot bot commented Nov 6, 2025

Uh oh!

erga-ear-bot bot commented Nov 12, 2025

Uh oh!

erga-ear-bot bot commented Nov 12, 2025

Uh oh!

erga-ear-bot bot commented Nov 12, 2025

Uh oh!

talioto commented Nov 13, 2025

Uh oh!

erga-ear-bot bot commented Nov 19, 2025

Uh oh!

erga-ear-bot bot commented Nov 19, 2025

Uh oh!

erga-ear-bot bot commented Nov 19, 2025

Uh oh!

auryjm commented Nov 19, 2025

Uh oh!

erga-ear-bot bot commented Nov 19, 2025

Uh oh!

auryjm commented Nov 19, 2025

Uh oh!

talioto commented Nov 20, 2025

Uh oh!

auryjm commented Nov 20, 2025

Uh oh!

talioto commented Nov 20, 2025

Uh oh!

erga-ear-bot bot commented Nov 27, 2025

Uh oh!

erga-ear-bot bot commented Dec 4, 2025

Uh oh!

erga-ear-bot bot commented Dec 11, 2025

Uh oh!

talioto commented Dec 19, 2025

Uh oh!

auryjm commented Dec 23, 2025

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

3 participants