US Market, Estimated Prices in USD (as of 2025)
The values below are **order-of-magnitude estimates** for the US market. Actual prices vary significantly based on service provider, project scale, and negotiated rates. Costs are based on **high-throughput platforms** (e.g., NovaSeq X, Revio) assuming high-plex runs, which lowers the per-sample cost. Costs for smaller projects on benchtop sequencers (e.g., MiSeq, MinION) will be different. Estimates **do not include labor, sample acquisition, or bioinformatics analysis**.
| Research Goal | Platform / Run Assumptions | Coverage / Depth | Est. Library Prep / Sample (USD) | Est. Sequencing / Sample (USD) | Est. Total / Sample (USD) |
|---|---|---|---|---|---|
| Genomics (DNA) Scenarios | |||||
| SNP/INDEL ID (Human, 3Gbp) | Illumina NovaSeq X Plus (multiplexing ~48 samples/run) | 30x | $80 - $150 | $400 - $650 | $480 - $800 |
| Population SNP ID (e.g., Plant) | Illumina NextSeq/NovaSeq (high-plex GBS/RAD) | n/a | $30 - $60 | $20 - $40 | $50 - $100 |
| *de novo* Assembly T2T (Human, 3Gbp) | PacBio Revio (1-2 SMRT Cells/sample) | 30x | $200 - $350 (HMW DNA) | $900 - $1,500 | $1,100 - $1,850 |
| *de novo* Assembly (Complex) | ONT PromethION (1-2 Flow Cells/sample) | 50x | $250 - $400 (HMW DNA) | $800 - $1,300 | $1,050 - $1,700 |
| Assembly Scaffolding | Hi-C (on Illumina NovaSeq) | ~500M reads | $400 - $600 | $800 - $1,200 | $1,200 - $1,800 |
| Transcriptomics (RNA) Scenarios | |||||
| Differential Gene Expression (DGE) | Illumina NextSeq/NovaSeq (multiplexed run) | 25M reads | $100 - $180 | $150 - $250 | $250 - $430 |
| Isoform Discovery & Quantification | PacBio Revio (multiplexed on SMRT Cell) | ~20M HiFi reads | $300 - $500 | $600 - $1,000 | $900 - $1,500 |
| RNA Modification Detection | ONT PromethION/GridION | ~15M reads | $350 - $550 (Direct RNA kit) | $400 - $700 | $750 - $1,250 |
| Single-Cell Gene Expression (3'/5') | 10x Genomics + Illumina NovaSeq | ~50k reads/cell | $2,000 - $3,500 (10k cells, 10x kit) | $2,500 - $4,000 | $4,500 - $7,500 |
| Epigenetics & Other Scenarios | |||||
| Global DNA Methylation (5mC) | WGBS on Illumina NovaSeq | 30x | $150 - $250 (bisulfite kit) | $500 - $800 | $650 - $1,050 |
| Comprehensive DNA Modifications | WGS on PacBio Revio / ONT PromethION | 30x | Cost is included in standard WGS (see Genomics). | ||
| Chromatin Accessibility | ATAC-Seq on Illumina NextSeq | ~50M reads | $200 - $350 | $200 - $300 | $400 - $650 |
| Metagenomics (Taxonomic Profile) | 16S rRNA Amplicon-Seq (Illumina MiSeq) | ~50k reads | $25 - $40 | $30 - $60 | $55 - $100 |
| Metagenomics (Functional Profile) | Shotgun Metagenomics (Long Read) | >20 Gbp | $250 - $400 | $600 - $1,000 | $850 - $1,400 |