dna barcode deconvulation strategy.

[Dan Kasney]

I would like to know how deconvulation of sequence files is being done.

Would appreciate if someone could guide me to a resource or process.

Supplementary note 2 mentions about it very briefly, would like a little more context.

[Jonathan Schmid-Burgk]

Hi Dan,

The deconvolution is currently implemented in most simple fashion, just count reads with perfect viral genome match, then increment a counter for the adjacent barcode, finally output a list of barcodes with their read numbers. I write all code in javascript as it's ok fast and runs on nearly every device

Best,

Jonathan

[David Li]

We have put up a tool to do this, available here: http://manuscript.lamp-seq.org/Inspector.htm. Lior Pachter's group has also implemented this using a "kallisto|bustools" workflow, see https://www.medrxiv.org/content/10.1101/2020.05.13.20100131v1.