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SeqDB

SeqDB is a web-based genomic data deposition and management platform for submitting, managing, and sharing sequencing data. It follows the ENA (European Nucleotide Archive) data model and provides an ENA-compatible API for programmatic access. Designed for NFDP genome and data science Dept at NFDP.

What is SeqDB?

SeqDB is a genomic data repository designed for:

  • Sequencing facilities depositing raw reads (FASTQ, BAM, CRAM)
  • Researchers submitting sample metadata with standardized checklists
  • Bioinformaticians downloading data programmatically via REST API
  • Data managers ensuring FAIR compliance and ENA interoperability

Key Features

Feature Description
ENA-style data model Project → Sample → Experiment → Run hierarchy
Bulk submission Upload TSV sample sheets with automatic file matching
File staging Upload files via browser or FTP before linking to samples
FAIR scoring Per-project Findable, Accessible, Interoperable, Reusable checks
Programmatic API ENA-compatible /filereport endpoint with download URLs
Metadata validation Checklist-based validation with cell-level error highlighting
Presigned downloads Secure, time-limited download URLs for all files

Data Model

The platform follows the ENA submission hierarchy:

Project (NFDP-PRJ-*)        ← Study-level metadata
  └── Sample (NFDP-SAM-*)       ← Organism, collection info
       └── Experiment (NFDP-EXP-*)  ← Sequencing platform, library
            └── Run (NFDP-RUN-*)      ← File, checksum, download

Comparison with ENA

Concept ENA SeqDB
File report endpoint GET /ena/portal/api/filereport?accession=...&result=read_run GET /api/v1/filereport?accession=...
Accession format ERR, ERS, ERX, ERP NFDP-RUN-*, NFDP-SAM-*, NFDP-EXP-*, NFDP-PRJ-*
Metadata checklists ERC000011, ERC000020, etc. Same checklist IDs
Bulk submission Webin spreadsheet upload TSV sample sheet upload
File download FTP / Aspera Presigned URLs (S3-compatible)
Response format TSV (default) JSON

Under Development

This platform is actively developed by the SeqDB team. For questions or contributions, see the Developer Guide.