The SeqDesk preprint is on bioRxiv

What the paper is about

The short version: a large fraction of sequencing studies is still published without the persistent, standards-compliant metadata that reuse depends on, and one big reason is that MIxS-compliant metadata is genuinely hard to assemble after the fact — environment-specific checklists can run to hundreds of fields. The paper describes SeqDesk’s answer: capture that metadata at project initiation, as part of the facility’s normal order intake, so FAIR-compliant public data becomes the natural output of routine operations rather than a chore bolted on at publication time.

The note walks through the pieces this site documents in depth:

• a configurable order-and-tracking system for sequencing projects,
• MIxS-compliant metadata capture, validated against ENA checklists at project initiation,
• bioinformatics analyses run through Nextflow pipelines,
• and brokered submission to the European Nucleotide Archive — all on the institution’s own infrastructure.

Its current scope is microbial sequencing data — metagenomes and isolate genomes, with the corresponding MIxS checklists — but the underlying checklist model is generic, so support can be extended to further data types and metadata standards beyond the microbial domain.

If you want the same story in interactive form, “How SeqDesk fits together” maps the architecture the paper describes, and “Up the wire” pulls apart the ENA submission step in detail.

How to cite