Documentation

O2A SEQUENCES ​

O2A SEQUENCES is the module of the O2A framework that manages metabarcoding samples, metadata, and sequences together: storing raw sequencing files (FASTQ), attaching harmonised sample metadata, running standardized analysis workflows, and generating submission-ready exports for public archives. Everything is organised by project: you select a project in the header, and files, workflows, and exports all scope to that project. Projects can be shared or made public, with role-based permissions. Sample metadata is held centrally in O2A SAMPLES (linked by shared persistent identifiers) and shared by every file linked to the same sample record.

O2A SEQUENCES holds active data only: once raw sequences are deposited in a long-term public archive they are removed locally, so the platform complements the public archives rather than duplicating them.

Metadata schema ​

The metadata schema conforms to the submission requirements of the European Nucleotide Archive (ENA) (www.ebi.ac.uk/ena), so that records created in O2A SEQUENCES can be submitted to ENA without further curation. It builds on the MIxS standard (Minimum Information about any Sequence) and the HARMONise schema (harmonise.awi.de), now incorporated into O2A SAMPLES, and every controlled field draws on the ENA/INSDC value lists. Fields designated mandatory by ENA are likewise required here; enforcing them is what keeps a record submission-ready for ENA and, via the GFBio broker, for the ASV Registry.

Required fields include:

  • Sample ID — identifies the sample and links the file to its record
  • Sample description
  • Taxon
  • Library layout (paired / single), source, strategy, and selection
  • Sequencing platform
  • Collection date
  • Location — latitude, longitude, country / sea, region and locality
  • Environment — biome, material, and feature

A record is considered complete only once all mandatory fields have been populated.

Import metadata ​

Metadata may be entered directly or imported from a prepared sheet.

Template download / upload. A metadata template (CSV, TSV, or XLSX) can be downloaded from the Files workspace, completed offline, and re-uploaded.

Inline editing. Values may be edited directly in the metadata table: rows are selected to enable editing and then saved or discarded. A "set whole column" control applies a single value to all selected rows.

Because metadata reside in O2A SAMPLES and are keyed by sample ID, a single edit propagates to all files that share that sample.

Import sequencing data ​

Raw reads are uploaded as FASTQ files (.fastq, .fq, or gzip-compressed .gz). Files are added by dropping them onto the upload area or selecting them manually, and are staged within the active project. Forward and reverse reads (R1 / R2) are paired automatically into a single sample entry by their filename suffix; a sample lacking one member of the pair is flagged as unpaired.

The required per-sample metadata are supplied during upload, either individually or in bulk from a metadata sheet. Checksums (md5) are not provided in the template but are computed after upload. Each file records its size, md5 checksum, upload time, associated sample, read direction, and paired file.

Export data ​

Exports are accessed from the exports view of the active project. O2A SEQUENCES generates submission-ready exports for three destinations: GFBio, ENA, and the ASV Registry. Two export types are available: a tabular metadata / FASTQ export in GFBio format, and a calculated-ASV export derived from a completed workflow.

ENA ​

European Nucleotide Archive (ENA) (www.ebi.ac.uk/ena)

GFBio ​

GFBio (www.gfbio.org)

ASV Registry (workflow required) ​

The calculated-ASV export publishes the standardized, provenance-tracked ASV (Amplicon Sequence Variant) table produced by an analysis workflow to the ASV Registry. A workflow is eligible only once it has completed successfully and produced an ASV table; workflows that are still running, have failed, or lack an ASV table cannot be exported. Running a workflow is therefore a prerequisite for this export.

Workflow ​

A workflow is a single execution of a pipeline over a defined set of input files within a project. Each pipeline runs as a containerized Docker analysis; pipelines implemented with established workflow managers (e.g. Nextflow, Snakemake) run unmodified within these containers, and additional pipelines can be integrated through the same standardized interface.