This site is generated from the maintained examples under docs/examples. It shows the current assay examples, read templates, and region templates.
Note. seqspec files are tightly tied to the data, assay design, sequencer, and library construction they describe. These examples are representative specs derived from Teichlab library structures. They are useful reference points, but they may be incomplete or incorrect for any one concrete assay or dataset that a user defines.
The assay pages below are rendered with seqspec print -f seqspec-html. Use the search box to filter the catalog.
| Name | Assay | Sequencer | Modalities | Date | Report | seqspec |
|---|---|---|---|---|---|---|
| 10x-ATAC | 10xATAC | Illumina | atac | 19 October 2018 | view | yaml |
| 10x-RNA-5prime | 10xRNA5prime | Illumina | rna | 2016-08-01 | view | yaml |
| 10x-ATAC-RNA | 10xMultiome | Illumina NovaSeq 6000 | rna, atac | 15 September 2020 | view | yaml |
| 10x-ATAC-RNA-MULTI/Illumina | 10x-ATAC-RNA-MULTI | Illumina NovaSeq 6000 | rna, atac, tag | 17 June 2019 | view | yaml |
| 10x-RNA-v1 | 10xRNAv1 | Illumina | rna | 15 April 2016 | view | yaml |
| 10x-RNA-v2 | 10xRNAv2 | Illumina | rna | 16 January 2017 | view | yaml |
| 10x-RNA-v3 | 10xRNAv3 | Illumina NovaSeq 6000 | rna | — | view | yaml |
| 10xCRISPR | 10xCRISPR | Illumina | crispr, rna | 10 June 2020 | view | yaml |
| 10xFB-3prime | 10xFB protein and RNA assay 3' | Illumina | rna, protein | 12 February 2018 | view | yaml |
| 10xFB protein and RNA assay 5' | 10xFB protein and RNA assay 5' | Illumina | rna, protein | — | view | yaml |
| 10xFB-VDJ-5prime | 10xVDJ and RNA 5' | Illumina | rna, vdj | 21 October 2016 | view | yaml |
| 10xv3 scrnaseq element adept truseq dual | element-adept-truseq-dual-index | Element Aviti | rna | 21 February 2024 | view | yaml |
| 10xv3 scrnaseq illumina truseq dual | Illumina-novaseq-truseq-dual-index | Illumina NovaSeq 6000 | rna | 21 February 2024 | view | yaml |
| BD-Rhapsody-EB | BD-Rhapsody-EB | Illumina | rna | 31 August 2022 | view | yaml |
| BD-Rhapsody-v1/Illumina | BD-Rhapsody-v1 | Illumina | rna | 20 December 2018 | view | yaml |
| CEL-Seq | CEL-Seq | Illumina | rna | 30 August 2012 | view | yaml |
| CEL-Seq2/Illumina | CEL-Seq2 | Illumina | rna | 28 April 2016 | view | yaml |
| DOGMAseq-DIG/Illumina | DOGMAseq-DIG | Illumina NovaSeq 6000 (S2 Reagent Kit v1.5) | protein, tag, rna, atac | 23 June 2022 | view | yaml |
| DOGMAseq-LLL/Illumina | DOGMAseq-LLL | Illumina NovaSeq 6000 (S2 Reagent Kit v1.5) | protein, rna, atac | 23 June 2022 | view | yaml |
| Drop-seq/Illumina | Drop-seq | Illumina | rna | 21 May 2015 | view | yaml |
| inDropv2/Illumina | Indropv2 | Illumina | rna | 08 December 2016 | view | yaml |
| ISSAAC-seq | issaac_seq | — | RNA, ATAC | 15 September 2020 | view | yaml |
| MARS-seq | mars_seq | — | RNA | 17 May 2019 | view | yaml |
| mcSCRB-seq | mcscrb_seq | — | RNA | 26 July 2018 | view | yaml |
| Microwell-seq | microwell_seq | — | RNA | 22 February 2018 | view | yaml |
| WT Mega v2 | WT-Mega-v2 | Illumina | rna | — | view | yaml |
| Pi-ATAC-seq | pi_atac_seq | — | ATAC | 02 November 2018 | view | yaml |
| PIPseq V2 | pipseqv2 | — | RNA | 06 March 2023 | view | yaml |
| PIPseq V3 | pipseqv3 | — | RNA | 06 March 2023 | view | yaml |
| Quartz-seq | quartz_seq | — | RNA | 17 April 2013 | view | yaml |
| Quartz-seq2 | quartz_seq2 | — | RNA | 09 March 2018 | view | yaml |
| CRISPRa_screening | sccrispra | NextSeq2000 p3 kit | rna, crispr | 28 March 2023 | view | yaml |
| sci-RNA-seq | sci_rna_seq | — | RNA | 18 August 2017 | view | yaml |
| sci-RNA-seq3 | sci_rna_seq3 | — | RNA | 20 February 2019 | view | yaml |
| scifi-RNA-Seq | scifi_rna_seq | — | RNA | 31 May 2021 | view | yaml |
| Seq-well | seq_well | — | RNA | 13 February 2017 | view | yaml |
| Seq-Well-S3 | seq_well_s3 | — | RNA | 02 July 2019 | view | yaml |
| SHARE-Seq | SHARE-Seq | Illumina | atac, rna | 23 October 2020 | view | yaml |
| Smart-seq2 | smart_seq2 | — | RNA | 02 January 2014 | view | yaml |
| Smart-seq3 | smart_seq3 | — | RNA_end, RNA_internal | 04 May 2020 | view | yaml |
| sn-m3C-seq | sn-m3C-seq | Illumina NextSeq500 | methyl, hic | 09 September 2019 | view | yaml |
| snmCT-seq | snmCT-seq | Illumina NextSeq500 | methyl, rna | 09 March 2022 | view | yaml |
| SPLiT-seq | split_seq | — | RNA | 15 March 2018 | view | yaml |
| STRT-seq | strt_seq | — | RNA | 05 April 2012 | view | yaml |
| STRT-seq-2i | strt_seq_2i | — | RNA | 27 November 2017 | view | yaml |
| STRT-seq-C1 | strt_seq_c1 | — | RNA | 27 April 2019 | view | yaml |
| SugarSeq/Illumina | SugarSeq | Illumina NextSeq | rna, tag | — | view | yaml |
| SureCell | surecell | — | RNA | 27 April 2019 | view | yaml |
| 10x Genomics | tang2009 | — | RNA | 06 April 2009 | view | yaml |
| template | template | — | mode | — | view | yaml |
| VASA-seq-drop | vasa_seq_drop | — | RNA | 27 June 2022 | view | yaml |
| VASA-seq | vasa_seq_plate | — | RNA | 27 June 2022 | view | yaml |