Table 1 Technologies currently available and settings used by UniverSC

From: A flexible cross-platform single-cell data processing pipeline

Parameter value

Technology [Platform, Vendor]

Barcode lengtha

UMI length

Reference

10x-v1

10x (version 1) [Chromium, 10x Genomics]

14

10

16b

10x-v2 (or 10x)

10x (version 2) [Chromium, 10x Genomics]

16

10

16b

10x-v3 (or 10x)

10x (version 3) [Chromium, 10x Genomics]

16

12

 

bravo

HyperCap [Bravo B, Agilent]

16

N/A

 

bd-rhapsody

BD Rhapsody [BD Rhapsody, BD]

27

8

 

fluidigm-c1

C1 [C1, Fluidigm]

16

N/A

 

c1-cage

C1 [Instrument C1]

16

N/A

20

c1-ramda-seq

C1 [Instrument: C1]

16

N/A

21

celseq

CEL-Seq

8

4

22,23

celseq2c

CEL-Seq2

6

6

23,24

dropseq

Drop-seq

12

8

6b

icell8-v2

ICELL8 (version 2) [ICELL8, Takara Bio]

11

N/A

7b

icell8

ICELL8 (version 3) [ICELL8, Takara Bio]

11

14

7b

icell8-5-prime

ICELL8 (version 3) [ICELL8, Takara Bio]

10

N/A

7b

icell8-full-length

ICELL8 (version 3) [ICELL8, Takara Bio]

16

N/A

7b

indrops-v1d,e

inDrop (version 1)

19

6

25,26

indrops-v2d,e

inDrop (version 2) [Vendor: 1CellBiof]

19

6

25,27

indrops-v3e,g

inDrop (version 3)

16

6

27

nadia

Nadia [Nadia, Dolomite Bio]

12

8

 

marsseq-v1

MARS-Seq

6

10

28

marsseq-v2

MARS-Seq 2.0

7

8

29

microwell

Microwell-Seq

18

6

30

quartz-seq

Quartz-Seq

6

N/A

31

quartz-seq2-1536

Quartz-Seq2 (1536 wells)

15

8

32

quartz-seq2-384

Quartz-Seq2 (384 wells)

14

8

32

ramda-seq

RamDA-Seq

6

N/A

33

sciseq2c,g

SCI-seq (2-level indexing)

30

8

1,34

sciseq3c,g

SCI-seq (3-level indexing)

40

8

1,34

scifiseq

scifi-seq

27

8

35

scrbseq

SCRB-Seq, mcSCRB-Seq

6

10

36,37

seqwell

plexWell [Vendor: seqWell]

12

8

38

smartseq

SMART-Seq (version 1)

16

N/A

39

smartseq2

SMART-Seq (version 2) [Vendor: Takara Bio]

16

N/A

40

smartseq2-UMI

SMART-Seq (version 2)

16

8

8,10b

smartseq3

SMART-Seq (version 3)

16

8

8,10b

splitseqc,d,h

SPLiT-Seq [Vendor: Parse BioSciences]

18

10

41

strt-seq

STRT-Seq

6

N/A

42

strt-seq-c1

STRT-Seq-C1

8

5

43

strt-seq-2i

STRT-Seq-2i

13

6

44

surecellh

SureCell [ddSEQ, Bio-Rad]

18

8

45,46

  1. aBarcode length is max or total (linkers are removed automatically where needed) excluding barcodes in the index files which requires demultiplexing.
  2. bTest data used in our study was generated from data this paper originally published.
  3. cThese technologies have their UMIs before their barcodes. The positions of UMIs and barcodes are automatically inverted when these technologies are selected as options.
  4. dThese technologies have their barcodes and UMIs in R2 rather than R1. The functional roles of R1 and R2 are automatically inverted when these technologies are selected as options.
  5. eThese technologies have their barcodes in two segments with Barcode-1 (8-11 bp) and Barcode-2 (8 bp). A barcode of 19 bp of the adjusted R1 file is used by filling in missing values with linker sequences.
  6. fVendor has since declared bankruptcy: http://1cellbio.com (Accessed April 1, 2020).
  7. gThese technologies have dual indexes (I1 and I2 from the i7 and i5 indexes from Illumina), which contain additional information on cell barcodes.
  8. hThese technologies have their barcodes in three segments with Barcode-1 (6 bp), Barcode-2 (6 bp), and Barcode-3 (6 bp). The first 18 bp of the adjusted R1 file is originally recognized as the cell barcode.
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