Assembly reviewing method using EARs
Using the quality control results of 1) the final step of the assembly pipeline, 2) the curation process, and 3) the final curated assembly, the ERGA Assembly Report pdf can be generated.
The pdf must be uploaded to the ERGA GitHub repo via a Pull Request to start the review process.
- Genomescope (mandatory) and Smudgeplot (optional) from your WGS accurate reads.
- gfastats, Merqury and BUSCO results for complete -pseudo-haplotypes (i.e., Hap1, Pri, collapsed, and also Hap2 if available) of the final pre and post-curation assembly steps.
- HiC contact maps for final post-curation -pseudo-haplotype(s) (Pretext or HiGlass): a PNG snapshot and a link for the .pretext files or folder (additional .mcool files are welcome) uploaded to the cloud (e.g., Nextcloud, Genomeark, etc). Important: it is crucial that the .pretext file shows bedgraph tracks like telomeric signal, gaps, coverage, etc. Also, it can be useful to provide a HiRes file too.
- Blobplot PNG snapshot for contamination screening for final post-curation -pseudo-haplotype(s).
- Notes (text) you have taken about the decontamination process, presence of plastids or symbionts, sample characteristics and quality, the curation process, observed haploid number, sex, etc.
- Data coverage
- Tools employed for assembly and curation, with version and key parameters used (optional, but recommended)