A list of more than 100 different single cell sequencing (omics) methods have been published. The large majority of methods are paired with short-read sequencing technologies, although some of them are compatible with long read sequencing.

List Method Reference Sequencing Mode Early Estimate Late EstimateTang methodShort Reads20082009CyTOFShort Reads20112012STRT-seq / C1Short Reads20112012SMART-seqShort Reads20122013CEL-seqShort Reads20122013Quartz-SeqShort Reads20122013PMA / SMAShort Reads20122013scBS-seqShort Reads20132014AbPairShort Reads20142014MARS-seqShort Reads20142015DR-seqShort Reads20142015G&T-seqShort Reads20142015SCTGShort Reads20142015SIDR-seqShort Reads20142015sci-ATAC-seqShort Reads20142015Hi-SCLShort Reads20152015SUPeR-seqShort Reads20152015Drop-ChipShort Reads20152015CytoSeqShort Reads20152016inDropShort Reads20152016sc-GEMShort Reads20152016scTrio-seqShort Reads20152016scM&T-seqShort Reads20152016PLAYRShort Reads20152016Genshaft-et-al-2016Short Reads20152016Darmanis-et-al-2016Short Reads20152016CRISP-seqShort Reads20152016scGESTALTShort Reads20152016CEL-Seq2 / C1Short Reads20152016STRT-seq-2iShort Reads20162017RNAseq @10xgenomicsShort Reads20162017RNAseq / Gene Expression @nanostringtechShort Reads20162017sc Targeted Gene Expression @fluidigmShort Reads20162017scTCR WafergenShort Reads20162017CROP-seqShort Reads20162017SiC-seqShort Reads20162017mcSCRB-seqShort Reads20162017Patch-seqShort Reads20162017Geo-seqShort Reads20162017scNOMe-seqShort Reads20162017scCOOL-seqShort Reads20162017CUT&RunShort Reads20162017MATQ-seqShort Reads20162017Quartz-Seq2Short Reads20172018Seq-WellShort Reads20172018DroNC-SeqShort Reads20172018sci-RNA-seqShort Reads20172018scATAC @10xgenomics Short Reads20172018scVDJ @10xgenomics Short Reads20172018scNMT triple omics Short Reads20172018SPLIT-seq Parse BiosciencesShort Reads20172018CITE-SeqShort Reads20172018scMNase-seqShort Reads20172018Chaligne-et-al-2018Short Reads20172018LINNAEUSShort Reads20172018TracerSeqShort Reads20172018CellTagShort Reads20172018ScarTraceShort Reads20172018scRNA-Seq Dolomite BioShort Reads20172018Trac-loopingShort Reads20172018Perturb-ATACShort Reads20182019scMethylationShort Reads20182019scHiCShort Reads20182019Multiplex Droplet scRNAseqShort Reads20182019sci-CARShort Reads20182019C1 CAGE single cellShort Reads20182019sc paired microRNA-mRNAShort Reads20182019scCAT-seqShort Reads20182019REAP-seq @fluidigmShort Reads20182019scCCShort Reads20182019yscRNA-SEQShort Reads20182019TARGET-seqShort Reads20182019MULTI-seqShort Reads20182019snRNA-seqShort Reads20182019sci-RNA-seq3Short Reads20182019BRIF-seqShort Reads20182019Drop-seq Dolomite BioShort Reads20182019Slide-seqShort Reads20182019CUT&TagShort Reads20182019CellTaggingShort Reads20182019DART-SeqShort Reads20182019scDamID&TShort Reads20182019ACT-seqShort Reads20182019Sci-Hi-CShort Reads20182019Slide-seqShort Reads20182019Simplified-Drop-seqShort Reads20182019scChIC-seqShort Reads20182019Dip-CShort Reads20182019CoBATCHShort Reads20182019Convert-seqShort Reads20182019Droplet-based scATAC-seqShort Reads20182019ECCITE-seqShort Reads20182019dsciATAC-seqShort Reads20182019CLEVER-seqShort Reads20182019scISOr-SeqShort Reads20182019MARS-seq2.0Short Reads20182019nano-NOMeLong Reads20182019MeSMLR-seqLong Reads20182019SMAC-seqLong Reads20182019MoonTag/SunTagShort Reads20182019SCoPE2Short Reads20182019sci-fateShort Reads20182019μDamIDShort Reads20182019Methyl-HiCShort Reads20182019RAGE-seqLong Reads20182019Paired-SeqShort Reads20182019Tn5PrimeShort Reads20182019NanoPAREShort Reads20182019BART-SeqShort Reads20182019scDam&T-seqShort Reads20182019itChIP-seqShort Reads20182019SNARE-seqShort Reads20182019ASTAR-seqShort Reads20182019sci-PlexShort Reads20182019MIX-SeqShort Reads20182019microSPLiTShort Reads20182019PAIso-seqShort Reads20182019FIN-SeqShort Reads20182019LIBRA-seqShort Reads20182019scifi-RNA-seqShort Reads20182019plexDIAShort Reads20212021scGET-seqShort Reads20222022MPXShort Reads20232023

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