10x Genomics libraries contain P5 and P7 adapters, which can be used for Illumina sequencing. 10x Genomics assays can also be modified to enable sequencing on various long- and short-read sequencing platforms, with some platforms requiring third-party analysis tools. Some variation in assay performance is expected based on the sequencer choice.
The 10x Genomics Compatible Products page contains a list of sequencing platforms compatible with 10x Genomics libraries.
The number of cycles required for each sequencing read, and the recommended sequencing read depth, can be found in the relevant User Guide.
The sequencers listed below have been verified as compatible with the indicated library type. Sequencer compatibility testing was performed either directly by 10x Genomics or by the Compatible Partner with data review by 10x Genomics.
Not all library types have been tested with every sequencer. For clarity, the table below indicates which library types were tested and which have not been tested. Compatibility cannot be guaranteed with library types that were not tested.
The Sequencing Handbook CG000809 contains additional resources for various 10x Genomics libraries, including:
- Number of cycles for reach read & read depth
- Loading concentration recommendation
- Index combinations for low plex pool
- Library pooling compatibilit
Compatible sequencers - short-read sequencing:
Illumina®
| 10x Genomics library type | Compatible Sequencer | Loading Concentration (pM)* | PhiX* (%) |
|---|---|---|---|
| 5’ v3 Gene Expression or V(D)J | MiSeq™ | 10 | 1 |
| NextSeq™ 500/550 | 1.6 | 1 | |
| NextSeq™ 1000/2000 | 650 | 1 | |
| NovaSeq™ 6000 Standard | 150 | 1 | |
| NovaSeq™ 6000 XP Workflow | 150 | 1 | |
| NovaSeq™ X Series | 150-200 | 1 | |
| 5’ v3 Cell Surface Protein or CRISPR Screening | Recommend pooling with 5’ Gene Expression libraries, using loading concentrations above | ||
| 5’ v2 / HT Gene Expression or V(D)J | MiSeq™ | 10 | 1 |
| NextSeq™ 500/550 | 1.5 | 1 | |
| NextSeq™ 1000/2000 | 650 | 1 | |
| NovaSeq™ 6000 Standard | 150 | 1 | |
| NovaSeq™ 6000 XP Workflow | 150 | 1 | |
| NovaSeq™ X Series | 150-200 | 1 | |
| 5’ v2 / HT Cell Surface Protein or CRISPR Screening | Recommend pooling with 5’ Gene Expression libraries, using loading concentrations above | ||
* Recommended loading concentrations and % PhiX are provided based on internal testing. These recommendations are suggested starting points and may need adjustments.
Ultima Genomics
| 10x Genomics library type | Compatible Sequencer | Notes |
|---|---|---|
| 5’ v3 / v2 Gene Expression | UG 100™ | Library conversion steps are required to add Ultima Genomics adapters. See Q&A article. |
| 5’ HT Gene Expression 5’ v3 / v2 / HT Cell Surface Protein, 5’ v3 / v2 / HT CRISPR Screening | Not tested | |
| 5’ v3 / v2 / HT V(D)J | Not compatible | Not compatible, see Q&A article. |
Element Biosciences
| 10x Genomics library type | Compatible Sequencer | Notes |
|---|---|---|
| 5’ v2 Gene Expression, 5’ v2 V(D)J | AVITI™ | Library conversion steps are required to add Element adapters. See Q&A article. |
| 5’ v3 / HT Gene Expression, 5’ v3 / HT V(D)J, 5’ v3 / v2 / HT Cell Surface Protein, 5’ v3 / v2 / HT CRISPR Screening | Not tested |
Compatible sequencers - long-read sequencing:
Oxford Nanopore Technologies (ONT)
| 10x Genomics assay | Compatible Sequencer | Notes |
|---|---|---|
| cDNA from 5’ v3 or v2 | PromethION™ | Amplified cDNA must be converted to ONT-compatible long-read libraries. See Q&A article. |
| cDNA from 5’ HT | Not tested |
Pacific Biosciences
| 10x Genomics assay | Compatible Sequencer | Notes |
|---|---|---|
| cDNA from 5’ v3 | Revio™ | Amplified cDNA must be converted to PacBio-compatible long-read libraries. See Q&A article. |
| cDNA from 5’ v2 | Sequel IIe™ | |
| cDNA from 5’ HT | Not tested |