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

Three sequencing services with published rate cards, targeted eDNA quoted per project, and the consulting that wraps around them. Rates are on the pricing page; everything else is scoped per request.

Priced services

• Voucher-linked specimen barcoding

  See pricing → Configure →

  Every specimen imaged, non-destructively extracted, COI-barcoded on Oxford Nanopore, and identified with a confidence rating. Other markers available.

  Bulk samples are imaged, triaged, and plated by BugPicker, our in-house picking robot — see it running on the lab bench →

• Environmental DNA (eDNA) metabarcoding

  See pricing → Configure →

  Community-level detection from water, soil, sediment, or air samples, one marker or several stacked on the same samples.

• Metagenome and metatranscriptome sequencing

  See pricing → Configure →

  All the DNA in a specimen, or the genes it and its microbes are actively using, on a dedicated long-read flow cell per specimen.

• Targeted eDNA (qPCR) for one or more species

  See pricing → Talk to us →

  Presence and abundance of specific species by qPCR, with custom assay development where no published assay exists.

Project-rate services

• Study design

  Talk to us →

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

• Bioinformatic data analysis and interpretation

  Talk to us →

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

• Custom eDNA / qPCR assay design and validation

  Talk to us →

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

• Field collection assistance

  Talk to us →

  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 through Press, part of BioKEA Works (currently in closed-testing alpha).

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.

What's the difference between barcoding, eDNA metabarcoding, metagenomics, and targeted qPCR?

Barcoding identifies individual physical specimens one at a time; eDNA metabarcoding detects whole communities from a water, soil, sediment, or air sample; metagenomics sequences everything living in and on a single specimen; targeted qPCR detects or measures one or a few named species with high sensitivity. Many programs combine them. Compare them side by side →

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.

BioInfoOS is also available directly, as part of BioKEA Works (currently in closed-testing alpha).

Know your sample count? Build an itemized quote in about a minute.