Susat2024

[MagdalenaHC]

Pull Request

This PR is for a

• New Publication(s)
• Correction

For the following list(s):

• ancientmetagenome-environmental (README)
• ancientmetagenome-hostassociated (README)
• ancientsinglegenome-hostassociated (README)

This is to close #1185

PR Workflow

1. Open this PR with sample metadata on the samples metadata sheet (:tada: you're already here!)
2. Wait for checks for sample metdata to pass
3. (If checks fail) make corrections, and push changes to this branch (no need to open a new PR!)
4. (Once passed) comment on this PR @spaam-bot please autofill <table_name> <project_id> to get a half-filled template! (may take a minute or so to get the comment with the file)
5. Fill in the template, and verify autofilled data correct!
6. Once filled in, append(!) the new rows from the TEMPLATE file to the end of the corresponding library metadata file, and update this PR
7. Wait for checks for library metadata to pass
8. Request review!

Pre-review checklist (new publications)

• Publication is published
  • Preprints currently not accepted?
• Checked the publication is not already in the database?
• Checked samples in this publication are not previously published data?
  • Newly re-sequenced metagenomes are OK!
• Samples are shotgun metagenomes and not amplicon data
  • Note: hostassociated-singlegenome may also contain whole-genome enriched data
• Checked the list follows conventions as described in the corresponding sample type's README file (e.g. using ERS/SRS accession codes for ENA/SRA)?
• Once sample table validation completed Library metadata has been added
  • Use @spaam-bot please autofill <table_name> <project_id> to get a half-filled template! May take a minute or so to get the comment with the file
  • Fill in template, and verify autofill data correct!
  • Once filled in, append(!) the new rows to the end of the corresponding library metadata file
• Changelog is updated to include the publication under 'Added'?

[jfy133]

Samples: perfect!
Libraries: perfect!

This is a perfect first submission (I think?), 👏 to you @MagdalenaHC ! Followed everything to a tee!

My only question is to verify that indeed it is all reads uploaded, because I see the submitted files as a) merged and b) in FASTA format:

ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR130/ERR13081219/KH200218_4.21Ord3287-S1-L1_S4_L002_001.merged.fa.gz

Which implies a certain amount of data processing , but if this isn't mapped or anything it should be fine

(Note for the future/your co-authors: uploaded data to ENA should not be merged if sequenced paired end!)

[MagdalenaHC]

Hi, the uploaded files are Clipped&Merged fasta format, no mapping or other processing has been done. Hope that helps.

[github-actions]

AMDirT, version 1.6.2

Samples

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_samples.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_samples.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_samples.tsv is valid

Libraries

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_libraries.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_libraries.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_libraries.tsv is valid

[jfy133]

This fell off my radar due to weeks of travelling and then sick kids, sorry @MagdalenaHC !

Thank you very much, this is good to go 👯