European Nucleotide Archive (ENA)

European Nucleotide Archive (ENA) provides a public repository and distribution service for nucleotide sequence data, enabling submission, archiving, search, and download of raw sequencing reads, genome assemblies, and functional annotations to support biological research and public‑health sequence sharing (including SARS‑CoV‑2 sequences).

Key Features:

• Supported data types: Hosts raw sequencing reads, genome assemblies, and functional annotations.
• Submission capabilities: Supports submission and publication of nucleotide sequence data and associated metadata.
• Programmatic access: Offers programmatic interfaces for automated submission, search, and data retrieval.
• Archiving and publishing: Provides persistent archiving and publication pathways for nucleotide sequence datasets.
• SARS‑CoV‑2 repository: Serves as a recommended open repository for SARS‑CoV‑2 genetic sequences.
• SARS‑CoV‑2 submission options: Provides single‑step submission for SARS‑CoV‑2 raw reads, tabular‑formatted metadata, and an option to remove human reads prior to submission.
• Tool packaging: Upload tools are packaged in Docker containers.
• Tool repositories: Includes a CLI ENA upload tool on GitHub (DOI 10.5281/zenodo.4537621), a Galaxy ENA upload tool available via ToolShed and GitHub (development version at https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload), and an ENA upload Galaxy container hosted by ELIXIR‑Belgium on GitHub (DOI 10.5281/zenodo.4730785).

Scientific Applications:

• Genomic surveillance and outbreak response: Enables deposition and sharing of pathogen sequences for public‑health surveillance, exemplified by SARS‑CoV‑2.
• Genome assembly deposition: Supports submission and archival of genome assemblies for comparative genomics and reference building.
• Data reproducibility and publication: Provides archival and publication of sequence data to support reproducible research and data citation.
• Pathogen raw‑read submission with host removal: Facilitates submission of pathogen raw reads with options to remove human reads prior to archive.

Methodology:

Provides single‑step submission for SARS‑CoV‑2 raw reads with tabular‑formatted metadata and an option to remove human reads prior to submission; upload tools are packaged in Docker and distributed as a CLI (GitHub, DOI 10.5281/zenodo.4537621), a Galaxy tool (ToolShed and GitHub development at https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload), and an ENA upload Galaxy container (ELIXIR‑Belgium, DOI 10.5281/zenodo.4730785).