Sequencing services for biodiversity research.

WHO IT'S FOR

• · Conservation nonprofits
• · State and federal agencies (DFW, USGS, NPS, EPA, NOAA)
• · Academic labs and graduate research programs
• · Environmental and ecological consultancies
• · Long-term biodiversity monitoring programs

CATALOG

What we offer

Project-rate engagements scoped per request. Tell us about your project and we'll come back with a quote — typically within a few days.

• Study design

  Best-practices consultation on sampling, replication, controls, and analysis.

• Bioinformatic data analysis and interpretation

  Read processing, taxonomy reconciliation, downstream statistics, written report.

• DNA-based identification of organisms (barcoding)

  Single-specimen barcode sequencing across COI, 16S, 18S, ITS, rbcL, matK, or custom primers.

• qPCR / eDNA assay (single + multi-species)

  Quantitative PCR for environmental DNA detection of one or more target species in water, soil, or sediment samples.

• Custom eDNA / qPCR assay design + validation

  New-species or cross-species assay design including primer/probe optimization and specificity validation.

• Metabarcoding, metagenomics, and other custom analyses

  Community-level amplicon surveys, shotgun metagenomics, hybrid assemblies, and bespoke pipeline integration.

• Field collection assistance

  Sampling protocol development and field collection support — Bay Area projects in person; remote consult elsewhere.

WHAT YOU GET BACK

FAIR-compliant data package by default.

• · Darwin Core Archive (DwC-A) deposit-ready package
• · GBIF (Global Biodiversity Information Facility) record
• · NCBI SRA (Sequence Read Archive) submission for raw reads
• · Zenodo DOI for the final data package
• · Written analysis report with methods, results, and provenance trail
• · Raw FASTQ + metadata on request for customers running their own pipelines

WORKFLOW

1. 01
   Discuss

   Free 30-minute scoping call. We help shape sampling design, primer choice, replication, and analysis goals — then send a written quote.

2. 02
   Send samples

   Shipping instructions, chain-of-custody manifest, and packaging guidance provided once a project is initiated. International samples accepted with appropriate import permits.

3. 03
   We sequence and analyze

   Samples flow through the BioKEA six-stage pipeline at the Berkeley LDC: extraction, prep, quantification, sequencing on the ONT Promethion 2, and bioinformatic analysis with full provenance.

4. 04
   Receive deliverables

   A FAIR-compliant data package — DwC-A, GBIF, SRA, Zenodo DOI — plus a written report. Optional interactive StoryMap publication on Agentis when it launches.

The internal six-stage pipeline that runs under every project — Ingest, Analyze, Draft, Review, Broadcast, Amplify — is documented in detail on the pipeline page.

FAQ

Common questions from sequencing customers

What's the typical turnaround time?

Typical projects complete in 4–8 weeks from sample receipt; custom assay design can extend timelines. We provide a project-specific timeline at quote.

What's the minimum sample volume or batch size?

Per-assay minimums vary. For eDNA water samples we typically accept 1–2 L filtered samples. For bulk specimens, 96-well-plate-compatible batches are most efficient. Single-specimen barcoding has no batch minimum.

Do you accept international samples?

Yes, with appropriate import permits and CITES documentation where required. We help first-time importers walk through the paperwork.

What primer choices are available for amplicon work?

Standard primers stocked: COI, 16S, 18S, ITS, rbcL, matK. Custom primer design is part of the eDNA / qPCR assay design service.

Are GBIF, NCBI SRA, and Zenodo deposits automatic?

Yes — they are part of the standard deliverable. Customers can request a hold or embargo on public deposits where institutional or publication considerations require it.

Can I use my own bioinformatic pipeline?

Yes. We can deliver raw FASTQ plus full metadata for downstream pipelines run by you or your collaborators. We also run our in-house BioinfoOS pipeline on request.