Does this tool support non-10x data or spatial transcriptome data types?

[PWD2]

Thank you for developing such a useful tool !

Does the tool support other data types besides 10x chromium single-cell?

For example, DNB-C4 single cell or spatial transcriptomes, 10x Visum, Stereo-seq, etc.

[mfansler]

Thanks for the interest! ❤️

Processing reads from alternate technologies is possible by changing the tech configuration option. The directly implemented parsing configurations can be queried with kallisto bus -l:

> kallisto bus -l 
List of supported single-cell technologies

short name       description
----------       -----------
10xv1            10x version 1 chemistry
10xv2            10x version 2 chemistry
10xv3            10x version 3 chemistry
CELSeq           CEL-Seq
CELSeq2          CEL-Seq version 2
DropSeq          DropSeq
inDropsv1        inDrops version 1 chemistry
inDropsv2        inDrops version 2 chemistry
inDropsv3        inDrops version 3 chemistry
SCRBSeq          SCRB-Seq
SureCell         SureCell for ddSEQ

If the technology is not in this list, then arbitrary parsing strategies can be specified as documented in the kallisto manual. For example, it looks like Visium (not HD) uses a technical R1 with 16 nt spatial barcode + 12 nt UMI. So, the specification for the tech parameter would look like:

tech: '0,0,16:0,16,28:1,0,0'

That is the code goes:

• 0,0,16: cell/spatial barcode is on the first read (0), in nucleotides 0...16 (not including end)
• 0,16,28: UMI is on the first read (0), in nucleotides 16...28 (not including end)
• 1,0,0: biological reads is on the second read (1), and includes all nucleotides (0,0)

Note that in this case, it is the same layout as '10xv3', so you could just use that. (Though, I expect the whitelist is not the same, so you would have to supply that separately.)

If there are particular technologies you are interested in, we could consider implementing a parser in the custom version of kallisto that we use. For example, I see that upstream has expanded their support and that shouldn't be much trouble to add in.

Hope that helps!

[PWD2]

Great! Thanks for your reply.