Contents:
- Getting Started
- Popular Services at a Glance
- New Instrumentation
- Extraction and Sample QC
- Library Preparation
- Sequencing
- Specialty Assays
- Proteomics (Olink)
- Bioinformatics
- Funding and Voucher Programs
- Good to Know
- Request Services
Getting Started
The Hubbard Center for Genome Studies is a full-service genomics core at the University of New Hampshire. We handle everything from nucleic acid extraction through sequencing and analysis, and we are happy to take on just one step or the whole project.
Not sure what you need? Start with a conversation, not a price list. Project consultation is free, and it is the single best thing you can do for your budget. We will help you choose a platform, work out how much sequencing depth your question actually requires, and find places to pool or scale that you may not have considered. Email us at unh.hcgs@unh.edu.
We also welcome grant-stage inquiries. If you need a letter of support or a quote for a proposal, we can turn one around quickly.
Popular Services at a Glance
Library preparation and sequencing are priced separately, because they behave differently. Preparation is a fixed cost per sample. Sequencing depends on how much depth your question needs, and we will help you work out how much that actually is.
If you send us purified DNA or RNA, the totals below are what you pay. If you would like us to extract for you, add $13 to $87 per sample depending on sample type, listed under Extraction and Sample QC.
Our move to the NovaSeq X Plus cut the cost per read to roughly a quarter of what it was on the NovaSeq 6000. A transcriptome that used to carry $250 of sequencing now carries about $63, and a microbial genome dropped from $100 to $25. Amplicon and PacBio pricing has changed little, because those are governed by read length and platform rather than by flow cell output.
| Service | Library prep | Sequencing | Total |
|---|---|---|---|
| Amplicon / Metabarcoding 16S, 18S, ITS, COI and other marker gene surveys | $20 PCR $10 + indexing $10 | $1 at 100 K reads, full plate | $21 |
| Multi-GBS SNP discovery and population genetics at scale | $24 library $14 + indexing $10 | $5 at 2 M reads | $29 |
| Illumina Whole Genome Microbial genomes, resequencing, variant calling | $71 | $25 at 10 M reads | $96 |
| Illumina Poly-A RNA Gene expression in eukaryotes | $157 | $63 at 25 M reads | $220 |
| Illumina Ribo-Depleted RNA Total RNA, non-coding RNA, degraded or prokaryotic | $164 | $63 at 25 M reads | $227 |
| PacBio Whole Genome (HiFi) De novo assembly, structural variants, repeats | $589 | $500 at 1 M HiFi reads | $1,089 |
| PacBio Full-Length Transcriptome Isoform discovery and full-length transcripts | $925 | $500 at 1 M HiFi reads | $1,425 |
Totals assume you supply purified nucleic acid; extraction is available as an add-on. Read counts are read pairs for Illumina and HiFi reads for PacBio. Illumina sequencing is on the NovaSeq X Plus. A $100 minimum sequencing charge applies per project, which is why the amplicon figure assumes a full 96-sample plate; smaller amplicon projects pay the $100 minimum. Every step is available separately and depth is adjustable. Prices are UNH internal rates; external academic and commercial rates are available on request. Bioinformatics is priced separately below.
New Instrumentation
We are in the middle of a significant instrument refresh, and the practical effect for users is that sequencing costs a fraction of what it used to.
- Illumina NovaSeq X Plus. Replacing our NovaSeq 6000. Per-read costs are roughly a tenth of what they were, which changes the calculus on sequencing depth for almost every project. Read lengths from 2 x 50 bp through 2 x 300 bp.
- PacBio Vega. Benchtop HiFi long-read sequencing, up to 60 Gb per SMRT Cell on a 24-hour run. Supports whole genome assembly and Kinnex full-length RNA.
Extraction and Sample QC
Extraction is an add-on to any of the services above. Our standard workflow uses MagMAX bead chemistry on a KingFisher system, which keeps handling to a minimum and gives consistent yields across large sample sets. High molecular weight extraction uses Nanobind chemistry to preserve fragment length for long-read applications.
| Service | Cost | Notes |
|---|---|---|
| DNA extraction | $13 | Automated, MagMAX and KingFisher |
| RNA extraction | $13 | Automated, MagMAX and KingFisher |
| DNA and RNA co-extraction | $18 | Both nucleic acids from a single sample |
| FFPE extraction | $36 | DNA and/or RNA from slides or blocks |
| High molecular weight DNA extraction | $87 | Nanobind, for PacBio and Omni-C |
| Fluorometric quantification (Qubit) | $3 | Per sample |
| Automated electrophoresis (TapeStation) | $10 | Per sample |
| Size selection (BluePippin) | $37 | Per sample |
| Library pooling and normalisation | $1 | Per library |
All prices per sample unless noted.
Library Preparation
| Service | Cost | Notes |
|---|---|---|
| DNA library (KAPA EvoPlus V2) | $71 | Enzymatic fragmentation, end repair, adapter ligation, dual indexing |
| DNA library, high throughput | $45 | Quarter-volume reactions, best value at 96 samples and above |
| Poly-A selected RNA library | $157 | mRNA capture for eukaryotic gene expression |
| Ribo-depleted RNA library | $164 | Total RNA including non-coding; suits degraded input |
| Small RNA library | $210 | miRNA and other small RNA species |
| Methyl-seq library | $108 | Enzymatic methyl sequencing |
| Amplicon PCR (one locus) | $10 | Includes gel verification and cleanup |
| Nested amplicon PCR | $20 | Two rounds of locus amplification |
| Indexing PCR | $10 | Adds dual indices to amplicons or GBS libraries |
| Multi-GBS library | $14 | Restriction digest and adapter ligation; pair with indexing PCR |
| Bacterial rRNA depletion | $67 | Add-on for prokaryotic transcriptomes |
| PacBio HiFi library | $589 | SMRTbell prep for whole genome sequencing |
| PacBio Kinnex full-length RNA library | $925 | Full-length transcript sequencing |
All prices per sample.
Sequencing
All Illumina sequencing is now on the NovaSeq X Plus, which replaced our NovaSeq 6000. Most users are best served by pooling into a shared run, and we handle the pooling, so you only pay for the depth you use.
Shared-run rates are based on the 1.5B flow cell, which is our standard format and the one most pooled projects run on. The 2 x 300 bp option uses 600-cycle chemistry and costs more per read; it is the right choice when read length matters, particularly for amplicons and metabarcoding.
Large projects can do considerably better. The 5B, 10B and 25B flow cells carry the same chemistry at far lower cost per read, so if your project can fill one, ask us for a dedicated flow cell quote rather than using the shared rate above.
Shared runs, priced by depth
| Configuration | Cost | Best for |
|---|---|---|
| Illumina, 2 x 150 bp NovaSeq X Plus, 1.5B flow cell | $2.50 per million read pairs | Genomes, transcriptomes, GBS, most applications |
| Illumina, 2 x 300 bp NovaSeq X Plus, 1.5B flow cell | $4.50 per million read pairs | Amplicons and metabarcoding, where read length matters |
| PacBio HiFi Vega, per SMRT Cell share | $500 per million HiFi reads | Long-read assembly and full-length transcripts |
Minimum sequencing charge of $100 per project. For low-depth work such as amplicon sequencing this is the effective floor, so those projects are most economical at 96 samples or more. PacBio pricing assumes the remainder of the SMRT Cell is filled; we will let you know if we need to hold your samples to combine with another project, or quote a dedicated cell.
Dedicated flow cells
Whole flow cells on the NovaSeq X Plus are available in 1.5B, 5B, 10B and 25B formats at 2 x 50, 2 x 100, 2 x 150 and 2 x 300 bp. Cost per read falls sharply with flow cell size: a dedicated 25B flow cell works out at well under half the shared-run rate. Contact us for a configuration recommendation and quote.
Specialty Assays
| Service | Cost | Notes |
|---|---|---|
| CUT&Tag | $158 | Chromatin profiling from low cell input; tagmentation in place |
| CUT&RUN | $203 | Chromatin profiling with broader target compatibility |
| Omni-C proximity ligation | $611 | Chromosome-scale scaffolding; endonuclease based, even coverage |
| Genome scaffolding analysis | $1,428 | Per genome, from Omni-C data |
| Single cell RNA-seq (Parse Evercode) | From $6,530 | Per kit. Mini, 100K and Mega formats; contact us to size a project |
Sequencing is quoted separately for these services, since depth varies widely by application.
Proteomics (Olink)
Olink uses proximity extension assay technology for highly multiplexed protein biomarker analysis from small sample volumes. We are the only certified Olink service provider in New England.
| Panel | Cost per sample | Batch size |
|---|---|---|
| Olink Explore HT over 5,300 proteins | $702 | 172 samples per kit |
| Olink Reveal approximately 1,000 proteins | $225 | 86 samples per kit |
Olink kits are fixed in size, so projects run in multiples of the batch size shown. If your sample count falls short of a full batch, get in touch and we will see whether we can combine you with another project.
Bioinformatics
Sequencing data is only useful once it is analysed. Our team builds custom pipelines and runs standard analyses, and we are glad to advise on analysis design before you generate the data rather than after.
| Analysis | Cost | Covers |
|---|---|---|
| RNA-Seq analysis | $2,380 | Up to 96 samples |
| RNA-Seq add-on: transcriptome assembly | $595 | Per project |
| RNA-Seq add-on: isoform analysis | $595 | Per project |
| Amplicon analysis | $200 + $10 | Per locus, plus per sample |
| Multi-GBS analysis | $1,785 | Up to 96 samples |
| Microbial WGS (assembly and annotation) | $595 | Up to 96 samples |
| Metagenomics I (assembly, MAGs, annotation) | $2,380 | Up to 96 samples, then $1,190 per additional 96 |
| Metagenomics II (functional annotation, PALADIN) | $1,190 | Up to 96 samples |
| Custom pipeline | $1,190 | Up to 96 samples |
| Consultation and custom analysis | $119 | Per hour |
Example: amplifying 16S and 18S from 96 samples is ($200 x 2) + ($10 x 96) = $1,360.
Funding and Voucher Programs
Several programs exist specifically to help cover the cost of core facility work in New Hampshire. If you are affiliated with any of the following, get in touch before you finalise a budget, because it may not need to come out of your own funds at all.
- NH-INBRE. Shared Resource Vouchers support core facility work for eligible faculty at partner institutions, on a rolling application. NH-INBRE funding opportunities
- NH-LIFT. The Core Facility Voucher Program expands access to research instrumentation across New Hampshire, and is open to both academic researchers and businesses. Reviewed on a rolling basis. NH-LIFT Core Facility Voucher Program
- CIBBR. Pilot Project awards support biomedical and bioengineering research at UNH, and applications that make use of UNH core facilities are viewed favourably. CIBBR Pilot Project Program
- USNH institutions. Researchers across the University System of New Hampshire are eligible for our internal rates. If you are at Keene State, Plymouth State or UNH Manchester and are not sure how to set up billing, just ask.
We are glad to help you put together the technical and budget sections of a voucher application, and we can provide a quote in whatever format the program requires. Email unh.hcgs@unh.edu.
Good to Know
- Larger batches cost less per sample. Automated extraction and library prep run in plate format, so a full plate is meaningfully cheaper per sample than a handful. If you are close to a plate boundary, it is worth asking.
- You control the sequencing budget. Depth is the biggest lever on cost, and more is not always better. We would rather help you pick the right depth than sell you reads you do not need.
- We invoice after the work is finished, never at the start of a project.
- Sample requirements vary by service. See our sample and shipping requirements, or ask us if your sample type is unusual. We work with environmental, marine, clinical and non-model organism samples routinely.
- Quotes for proposals are free. We can provide a letter of support and a detailed budget for grant submissions.
- Prices are reviewed annually and confirmed at the time work is scheduled. For projects starting in a future fiscal year, we will reconfirm before beginning.
Request Services
To get started, fill out the form below. If you would rather talk it through first, email unh.hcgs@unh.edu and we will get back to you.
