Getting your assembly reviewed using the EAR

Once you have your EAR, to request a formal review of your species' assembly, follow the procedure detailed below:

1.

Fork the ERGA-consortium/EARs repo (only the main branch is necessary)

---

---

2.

Now on YOUR_ID/EARs repo, enter the Assembly_Reports folder

---

---

3.

Prepare a folder and subfolder with your species name and ToLID, respectively, to place your EAR pdf, i.e., Species_name/ToLID/ToLID_EAR.pdf

---

4.

Upload the folders with the EAR pdf into the Assembly_Reports folder of YOUR_ID/EARs repo (the resulting file will be inside the Assembly_Reports folder, e.g., Assembly_Reports/Caretta_caretta/rCarCar2/rCarCar2_EAR.pdf).

---

---

Commit the changes to a new branch specific to this species EAR (e.g., myToLID_EAR_branch. See example below).

Important! If you want to submit more than one species, you must have one branch per each.

---

5.

Create a Pull Request from repo: YOUR_ID/EARs | branch: myToLID_EAR_branch to repo: ERGA-consortium/EARs | branch: main

A template should appear in the Pull Request description for you to complete all the fields (valid projects are ERGA-BGE, ERGA-Pilot and ERGA-Community).

---

6.

When the Pull Request is placed, the reviewing process starts. A reviewer will be assigned, and all the communications will happen inside the same Pull Request chat. Like in every other working space, we follow the ERGA Code of Conduct during the reviewing process.

Outcome

✅ If everything looks good, the assembly will be approved to be uploaded to ENA under the ERGA project umbrella, and the EAR will now be part of the stable ERGA repository of assembly reports.

❌ If the reviewer thinks something should be clarified, addressed or corrected, it will be requested through the communication channel opened during the Pull Request. Notice that, unless it is explicitly required, another Pull Request should NOT be opened to update the PDF. Any updates on the PDF should be done in the repo: YOUR_ID/EARs | branch: myToLID_EAR_branch, and they will be automatically translated to the current Pull Request.

BGE contig-level assembly

For the BGE project, if the data are not good enough to produce a high-quality chromosome-level assembly, you may submit an EAR for project-reporting purposes that will not be assessed by reviewers.

In this case, proceed as follows. For example, if you only achieved a contig-level assembly:

• Complete the SAMPLE INFORMATION, SEQUENCING DATA, and GENOME PROFILING DATA sections as usual (you may remove the Smudgeplot section if it was not used).
• ASSEMBLY DATA section:
  • Pre-curation results (gfastats, BUSCO, and Merqury) should be based on the contig-level assembly.
  • Post-curation should contain the same contig-level assembly results (gfastats, BUSCO, and Merqury). You may leave the hic_FullMap_png and hic_FullMap_link fields empty.
  • It is advisable to run decontamination tools (FCS-GX, BlobTools) to provide additional context. If a BlobPlot was produced, add the path to blobplot_cont_png, otherwise, leave it empty.
• In the METHODS DATA section, complete the Assembly subsection as far as you reached. You may remove the Curation subsection if there is nothing to report.
• Complete the CURATION NOTES with the information that you have.

⚠️ IMPORTANT when submitting this contig-level EAR to the Github repo: When opening a PR, do not use the template fields (ToLID, Species, Project, Affiliation). Instead, leave the body empty or just add an explanation of this particular case in a couple of sentences. This will prevent the bot from picking up the PR in the usual way, and the case will be handled by a supervisor.