jaActMedi1 EAR

[fcamara7]

Assembly review request

• ToLID: jaActMedi1
• Species: Actinia mediterranea
• Project: ERGA-BGE
• Affiliation: CNAG

[erga-ear-bot]

Hi @fcamara7, thanks for sending the EAR of Actinia mediterranea.
I added the corresponding tag to the PR and will contact a supervisor and a reviewer ASAP.

[erga-ear-bot]

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

[additive3]

ok From: "erga-ear-bot[bot]" ***@***.***> Reply to: ERGA-consortium/EARs ***@***.***> Date: Tuesday 18 February 2025 at 10:43 To: ERGA-consortium/EARs ***@***.***> Cc: Jo Wood ***@***.***>, Mention ***@***.***> Subject: Re: [ERGA-consortium/EARs] jaActMedi1 EAR (PR #158) [EXT] Hi @additive3 [github.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_additive3&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=TUaG6OqjPfI1I0rzJIbKqE8Tjv85ynPYIkNbCjRS2SI&m=vjxCHRmp9zfAv0i4S3JmTt4Zd7R-2tUfaTr1ebVwfID6K0FT-UbMtLO-vp4QNXrk&s=8mpHhZy-nrtNi5dQ-JTnS1ZeF-A7BlBAHXxmUvJfmw4&e=>, do you agree to supervise [github.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_ERGA-2Dconsortium_EARs_wiki_Assignees-2Dsection&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=TUaG6OqjPfI1I0rzJIbKqE8Tjv85ynPYIkNbCjRS2SI&m=vjxCHRmp9zfAv0i4S3JmTt4Zd7R-2tUfaTr1ebVwfID6K0FT-UbMtLO-vp4QNXrk&s=nd3BBZ_ECif2E_x3KLs8WuT01h5H-cduR86lw9hJtjg&e=> this assembly? Please reply to this message only with OK to give acknowledge. — Reply to this email directly, view it on GitHub [github.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_ERGA-2Dconsortium_EARs_pull_158-23issuecomment-2D2665259878&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=TUaG6OqjPfI1I0rzJIbKqE8Tjv85ynPYIkNbCjRS2SI&m=vjxCHRmp9zfAv0i4S3JmTt4Zd7R-2tUfaTr1ebVwfID6K0FT-UbMtLO-vp4QNXrk&s=2eY9oMhe0R5vj23GdhH4Q1eUYqZoXL-vDDjdGwMsGH4&e=>, or unsubscribe [github.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AEFJV4PDFC2G4KNFEOU76632QMFGRAVCNFSM6AAAAABXLJRVHGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMNRVGI2TSOBXHA&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=TUaG6OqjPfI1I0rzJIbKqE8Tjv85ynPYIkNbCjRS2SI&m=vjxCHRmp9zfAv0i4S3JmTt4Zd7R-2tUfaTr1ebVwfID6K0FT-UbMtLO-vp4QNXrk&s=hwnQzgyHAbeFSgRpYReGArlrWZppsrtr1esfECYxQ6w&e=>. You are receiving this because you were mentioned.Message ID: ***@***.***> [Image removed by sender. erga-ear-bot[bot]]erga-ear-bot[bot] left a comment (ERGA-consortium/EARs#158) [github.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_ERGA-2Dconsortium_EARs_pull_158-23issuecomment-2D2665259878&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=TUaG6OqjPfI1I0rzJIbKqE8Tjv85ynPYIkNbCjRS2SI&m=vjxCHRmp9zfAv0i4S3JmTt4Zd7R-2tUfaTr1ebVwfID6K0FT-UbMtLO-vp4QNXrk&s=2eY9oMhe0R5vj23GdhH4Q1eUYqZoXL-vDDjdGwMsGH4&e=> Hi @additive3 [github.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_additive3&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=TUaG6OqjPfI1I0rzJIbKqE8Tjv85ynPYIkNbCjRS2SI&m=vjxCHRmp9zfAv0i4S3JmTt4Zd7R-2tUfaTr1ebVwfID6K0FT-UbMtLO-vp4QNXrk&s=8mpHhZy-nrtNi5dQ-JTnS1ZeF-A7BlBAHXxmUvJfmw4&e=>, do you agree to supervise [github.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_ERGA-2Dconsortium_EARs_wiki_Assignees-2Dsection&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=TUaG6OqjPfI1I0rzJIbKqE8Tjv85ynPYIkNbCjRS2SI&m=vjxCHRmp9zfAv0i4S3JmTt4Zd7R-2tUfaTr1ebVwfID6K0FT-UbMtLO-vp4QNXrk&s=nd3BBZ_ECif2E_x3KLs8WuT01h5H-cduR86lw9hJtjg&e=> this assembly? Please reply to this message only with OK to give acknowledge. — Reply to this email directly, view it on GitHub [github.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_ERGA-2Dconsortium_EARs_pull_158-23issuecomment-2D2665259878&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=TUaG6OqjPfI1I0rzJIbKqE8Tjv85ynPYIkNbCjRS2SI&m=vjxCHRmp9zfAv0i4S3JmTt4Zd7R-2tUfaTr1ebVwfID6K0FT-UbMtLO-vp4QNXrk&s=2eY9oMhe0R5vj23GdhH4Q1eUYqZoXL-vDDjdGwMsGH4&e=>, or unsubscribe [github.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AEFJV4PDFC2G4KNFEOU76632QMFGRAVCNFSM6AAAAABXLJRVHGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMNRVGI2TSOBXHA&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=TUaG6OqjPfI1I0rzJIbKqE8Tjv85ynPYIkNbCjRS2SI&m=vjxCHRmp9zfAv0i4S3JmTt4Zd7R-2tUfaTr1ebVwfID6K0FT-UbMtLO-vp4QNXrk&s=hwnQzgyHAbeFSgRpYReGArlrWZppsrtr1esfECYxQ6w&e=>. You are receiving this because you were mentioned.Message ID: ***@***.***>

…

---------------------------------------------------------------------- The Wellcome Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA.

[erga-ear-bot]

*****
EAR Reviewer Selection Process
Date: 2025-02-18 10:51

All Eligible Candidates:

Github ID  | Full Name      | Institution | Total Reviews | Last Review | Active | Busy | Calling Score | Adjusted Score
------------------------------------------------------------------------------------------------------------------------
tommathers | Tom Mathers    | Sanger      | 4             | 2025-02-13  | Y      | N    | 1005          | 1055          
additive3  | Jo Wood        | Sanger      | 4             | 2024-11-04  | Y      | N    | 1005          | 1050          
tbrown91   | Tom Brown      | IZW         | 9             | 2024-10-31  | Y      | N    | 993           | 988           
diegomics  | Diego De Panis | IZW         | 8             | 2024-10-22  | Y      | N    | 991           | 986           

Selected reviewer: Tom Mathers (tommathers)
The decision was based on:
- different institution ('Sanger')
- active ('Y')
- not busy ('N')
- highest adjusted calling score in this particular selection (1055)

[erga-ear-bot]

Hi @tommathers, do you agree to review this assembly?
Please reply to this message only with Yes or No by 24-Feb-2025 at 15:51 CET

[tommathers]

Yes Dr. Thomas Mathers Senior Computer Biologist Genome Reference Informatics Team Tree of Life Wellcome Sanger Institute Hinxton Cambridge CB10 1SA Twitter: @Thomas_Mathers [twitter.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__twitter.com_Thomas-5FMathers-3Flang-3Den-2Dgb&d=DwMGaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=MigC00eCez0AYiD8Bi3uR5vUblihAN7OJ3KK8sbnotw&m=tJRHixSYq-VP6FIxTiP35xdkMZl3FaXQVx1qay3XZ-7I4UkhUxDC7h1P98bVhcBb&s=hffLCC65eIfPsnmm3hnO-CV4DYCZYG2ebSippldU3zw&e=> Publications: Google Scholar [scholar.google.co.uk]<https://urldefense.proofpoint.com/v2/url?u=https-3A__scholar.google.co.uk_citations-3Fhl-3Den-26user-3D5XjBm94AAAAJ-26view-5Fop-3Dlist-5Fworks-26sortby-3Dpubdate&d=DwMFAg&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=MigC00eCez0AYiD8Bi3uR5vUblihAN7OJ3KK8sbnotw&m=KIKynKbLKfS4YVQYVctJHL39ls39CbRogxK7G0OumbwWdwS4Qdlkrg9NnRJHPJGs&s=T2pa4qY1i623xxULQ3x4gTTj4JvNcKbwYHoNm5knTFc&e=> From: "erga-ear-bot[bot]" ***@***.***> Reply to: ERGA-consortium/EARs ***@***.***> Date: Tuesday 18 February 2025 at 10:51 To: ERGA-consortium/EARs ***@***.***> Cc: Thomas Mathers ***@***.***>, Mention ***@***.***> Subject: Re: [ERGA-consortium/EARs] jaActMedi1 EAR (PR #158) [EXT] Hi @tommathers [github.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_tommathers&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=MigC00eCez0AYiD8Bi3uR5vUblihAN7OJ3KK8sbnotw&m=8m490V3pFzCtiY9bR7H_GjbMhkCufoGXBMffqta0N8AMnrxKPZRSaoCKaq329uV3&s=exxsC5Me5LOFx_qzgSvJ4C1PFs3NYCHQfJSCjJM4Tuo&e=>, do you agree to review this assembly? Please reply to this message only with Yes or No by 24-Feb-2025 at 15:51 CET — Reply to this email directly, view it on GitHub [github.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_ERGA-2Dconsortium_EARs_pull_158-23issuecomment-2D2665278913&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=MigC00eCez0AYiD8Bi3uR5vUblihAN7OJ3KK8sbnotw&m=8m490V3pFzCtiY9bR7H_GjbMhkCufoGXBMffqta0N8AMnrxKPZRSaoCKaq329uV3&s=NqJ9bgpjF-2xI83VaEgzecBtPrbw6d2PmJKiyH0FDO4&e=>, or unsubscribe [github.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_ABVP3GZYHAL6G5HKBJOUMP32QMGDZAVCNFSM6AAAAABXLJRVHGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMNRVGI3TQOJRGM&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=MigC00eCez0AYiD8Bi3uR5vUblihAN7OJ3KK8sbnotw&m=8m490V3pFzCtiY9bR7H_GjbMhkCufoGXBMffqta0N8AMnrxKPZRSaoCKaq329uV3&s=tT2p8-S6ZagzGcrjLsFYmbQtL-w8YTkM65MFu2q7jw4&e=>. You are receiving this because you were mentioned.Message ID: ***@***.***> [Image removed by sender. erga-ear-bot[bot]]erga-ear-bot[bot] left a comment (ERGA-consortium/EARs#158) [github.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_ERGA-2Dconsortium_EARs_pull_158-23issuecomment-2D2665278913&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=MigC00eCez0AYiD8Bi3uR5vUblihAN7OJ3KK8sbnotw&m=8m490V3pFzCtiY9bR7H_GjbMhkCufoGXBMffqta0N8AMnrxKPZRSaoCKaq329uV3&s=NqJ9bgpjF-2xI83VaEgzecBtPrbw6d2PmJKiyH0FDO4&e=> Hi @tommathers [github.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_tommathers&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=MigC00eCez0AYiD8Bi3uR5vUblihAN7OJ3KK8sbnotw&m=8m490V3pFzCtiY9bR7H_GjbMhkCufoGXBMffqta0N8AMnrxKPZRSaoCKaq329uV3&s=exxsC5Me5LOFx_qzgSvJ4C1PFs3NYCHQfJSCjJM4Tuo&e=>, do you agree to review this assembly? Please reply to this message only with Yes or No by 24-Feb-2025 at 15:51 CET — Reply to this email directly, view it on GitHub [github.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_ERGA-2Dconsortium_EARs_pull_158-23issuecomment-2D2665278913&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=MigC00eCez0AYiD8Bi3uR5vUblihAN7OJ3KK8sbnotw&m=8m490V3pFzCtiY9bR7H_GjbMhkCufoGXBMffqta0N8AMnrxKPZRSaoCKaq329uV3&s=NqJ9bgpjF-2xI83VaEgzecBtPrbw6d2PmJKiyH0FDO4&e=>, or unsubscribe [github.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_ABVP3GZYHAL6G5HKBJOUMP32QMGDZAVCNFSM6AAAAABXLJRVHGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMNRVGI3TQOJRGM&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=MigC00eCez0AYiD8Bi3uR5vUblihAN7OJ3KK8sbnotw&m=8m490V3pFzCtiY9bR7H_GjbMhkCufoGXBMffqta0N8AMnrxKPZRSaoCKaq329uV3&s=tT2p8-S6ZagzGcrjLsFYmbQtL-w8YTkM65MFu2q7jw4&e=>. You are receiving this because you were mentioned.Message ID: ***@***.***>

…

---------------------------------------------------------------------- The Wellcome Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA.

[erga-ear-bot]

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.

[additive3]

Hi @fcamara7

The pretext map file hosted is on a drive I am unable to access, can you rectify please.

Best,
Jo

[fcamara7]

Hi @fcamara7

The pretext map file hosted is on a drive I am unable to access, can you rectify please.

Best, Jo

I am sorry @additive3 @tommathers I thought I had given global access to the foder..You should have full access to the folder now through the link below. Thanks a lot!
https://ccnag-my.sharepoint.com/:f:/g/personal/tyler_alioto_cnag_eu/Eqxd0WmBivlOkVqH5d5NEQMBtt72ScmhnNTfJiXrRdWO5g?e=ZzanCC

[additive3]

Thanks @fcamara7, have access now!

[additive3]

Hi @fcamara7

Assembly looks pretty good, but I believe there are some things that need altering.
First though I think you are hampering your curation efforts by running with MQ40, especially in repetitive regions where you have a complete absence of data. Mapping/displaying multi aligning reads really aids understanding :)

SUPER_8 break 6.38Mb move to end and incoprorate scaffold_23 (SUPER_8_2, scaffold_23 -ve , SUPER_8_1)
SUPER_13 break 12.25Mb move to start (SUPER_13_2, SUPER_13_1)
SUPER_17 break 5.12Mb flip (SUPER_17_1 -ve , SUPER_17_2)

I also believe that the following changes are needed but the information is currently incomplete so there is some ambiguity and perhaps I am over-seeing/thinking...

SUPER_7 break 420kb, insert -ve @3.9Mb
SUPER_9 break 13.26Mb flip end. (SUPER_9_1, SUPER_9_2 -ve )
SUPER_19 break 5.37Mb flip end (SUPER_19_1, SUPER_19_2 -ve )

[fcamara7]

Hi @fcamara7

Assembly looks pretty good, but I believe there are some things that need altering. First though I think you are hampering your curation efforts by running with MQ40, especially in repetitive regions where you have a complete absence of data. Mapping/displaying multi aligning reads really aids understanding :)

SUPER_8 break 6.38Mb move to end and incoprorate scaffold_23 (SUPER_8_2, scaffold_23 -ve , SUPER_8_1) SUPER_13 break 12.25Mb move to start (SUPER_13_2, SUPER_13_1) SUPER_17 break 5.12Mb flip (SUPER_17_1 -ve , SUPER_17_2)

I also believe that the following changes are needed but the information is currently incomplete so there is some ambiguity and perhaps I am over-seeing/thinking...

SUPER_7 break 420kb, insert -ve @3.9Mb SUPER_9 break 13.26Mb flip end. (SUPER_9_1, SUPER_9_2 -ve ) SUPER_19 break 5.37Mb flip end (SUPER_19_1, SUPER_19_2 -ve )

thanks @additive3 ! , will take a look and get back to you asap.

[tommathers]

Hi @fcamara7. Sorry for the delay. Just tried to download the file and I dont have permission.

[erga-ear-bot]

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