This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Molecular Loop ONT Demultiplexing

Hello,

Does anyone have an existing pipeline or bioinformatic workflow for demultiplexing data generated using the Molecular Loop protocol and the Oxford Nanopore (ONT) platform?

Specifically, I am using the multiplex viral RNA target capture protocol with ONT sequencing.

Thank you! Tillie Dunham

demultiplexing molecular ont loop
• 49 views • link
written by Tillie • Tillie

What kind of data do you have?

it seems that protocol is discontinued from ONT since mid 2026. From what I remember that downstream analysis was done/included in the GridION-minKNOW machine and ONT never released a standalone workflow for it?

• 0 views • link
written by lieven.sterck lieven.sterck

Thank you for your reply! I am using the multiplex viral RNA target capture (ONT) protocol from molecular loop to create a single pooled sample that I will take into ONT library prep using the ligation sequencing kit (https://nanoporetech.com/document/ligation-sequencing-amplicons-sqk-lsk114). I am also planning to sequence on the GridION device and will likely be using Dorado for base calling.

From my understanding, the typical demultiplexing done on the GridION using minKNOW will not work for this application since the indexing is done within the molecular loop protocol. I have a list of the index sequences that will be used in the molecular loop protocol but am unsure how to go about demultiplexing after ONT sequencing.

Sheet with index sequences: https://molecularloop.com/wp-content/uploads/2025/05/ML2100-ON_Product-Data-Sheet_v1.pdf

I am also waiting to see if I can get a URL for the molecular loop protocol and will reply again when I have that protocol.

Any feedback is welcomed and highly appreciated!

Tillie Dunham

• 0 views • link
written by Tillie • Tillie

0 answers

No answers yet.

Log in to answer this question.

More posts like this