Research Object Crate for ENA Reads and Assembly Submission Workflow

# ENA Reads & Assembly Submission Workflow Originally developed within the [EVORA project](https://evora-project.eu/), this two-step Galaxy workflow streamlines submissions to the [European Nucleotide Archive (ENA)](https://www.ebi.ac.uk/ena). The workflow first submits raw sequencing reads via the **Galaxy ENA upload tool**, then submits assembled sequences using the **Galaxy ENA Webin CLI tool**. The process is fully interactive and GUI-driven while retaining ENA’s required validations leveraging the user-scoped credential management system and the data upload/management from Galaxy. ## Step 1 — Raw reads: Galaxy ENA upload tool A Galaxy wrapper around the [ENA-upload-cli](https://github.com/usegalaxy-eu/ena-upload-cli) that brings a graphical interface and interactive checks to standard ENA read submissions. **Key features** - Raw read submission with ENA-upload-cli at its core - Use [tabular or excel sheet templates](https://github.com/ELIXIR-Belgium/ENA-metadata-templates) to easily capture the metadata - Client side validation using ENA checklists - Create, add, and modify ENA objects (e.g., studies, experiments, samples, runs) ## Step 2 — Consensus sequences: Galaxy ENA Webin CLI A Galaxy wrapper around ENA’s [Webin-CLI](https://github.com/enasequence/webin-cli) for interactive submission of consensus sequences, with full checklist coverage. **Key features** - Seamless integration with the Galaxy ENA upload tool to fetch and reuse metadata - Interactive metadata submission and validation - Support for all assembly levels (contig, scaffold and chromosome) ## Funding The EVORA project has received funding from the European Union's HORIZON programme under grant agreement No 101131959

Author

Bert Droesbeke

License

MIT

Contents