dna barcode deconvulation strategy.

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Dan Kasney

May 17, 2020, 8:45:21 PM5/17/20
to LAMP-Seq
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

May 18, 2020, 5:47:58 PM5/18/20
to LAMP-Seq
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


David Li

Jun 11, 2020, 12:15:27 AM6/11/20
to LAMP-Seq
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.
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