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Regulatory Data Submission (ENA/GEO/SRA) Training | Metadata, Webin-CLI, SRA Toolkit & Validation

NTHRYS >> Services >> Academic Services >> Training Programs >> Bioinformatics Training >> Genomics, Transcriptomics, Molecular Systems >> Regulatory Data Submission (ENA/GEO/SRA) Training | Metadata, Webin-CLI, SRA Toolkit & Validation

Regulatory Data Submission — ENA / GEO / SRA

Master compliant submission of genomics datasets to ENA, GEO and SRA with standards driven metadata, validation, accessioning, transfer automation and auditable reports.

Regulatory Data Submission (ENA / GEO / SRA)
Help Desk · WhatsApp
Session 1
Fee: Rs 6300
Standards, Accessions & Compliance
  • Repository landscape, policy and ethics: consent and data access
    • Theory
  • Standards and checklists: MINSEQE, MIxS, BioProject/BioSample models
    • MINSEQE MIxS BioProject BioSample
  • Accession types, identifiers and file formats for raw and processed data
    • FASTQ/BAM SOFT/MINiML TSV/XML MD5
Session 2
Fee: Rs 8400
Metadata Templates & Validation
  • Create and validate ENA Webin templates for study, sample, experiment and run
    • Webin-CLI ENA validator ebi-ena-cli
  • GEO metadata sheets, SOFT/MINiML packing and series/sample linking
    • GEOparse GEOmetadb checklists
  • Controlled vocabularies, ORCID, grant IDs and data use restrictions
    • OBO terms ORCID DUO
Session 3
Fee: Rs 11200
ENA, GEO, SRA Submission Workflows
  • Raw data transfer with Aspera or FTP and checksum verification
    • Aspera lftp/FTP md5sum/sha256sum
  • SRA Toolkit based packing and submission helpers
    • SRA Toolkit vdb-validate prefetch/fastq-dump
  • Error handling, retractions, updates and linking to publications
    • helpdesk tickets accession merges PMID/DOI links
Session 4
Fee: Rs 14000
Mini Capstone: Submit & Report
  • Design an end to end packaging and submission workflow with provenance
    • Theory
  • Automate prepare → validate → transfer → submit → confirm → report
    • Snakemake Conda/Mamba Quarto/JupyterLab
  • Deliver accession list, checksums, logs and submission ready documentation
    • pandas CSV/TSV exports PDF bundle


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