Post

Ragnar {Groot Koerkamp}
@curiouscoding.nl

Really exciting that the preprint on Barbell, a new demultiplexer, is finally out! It's the first tool that builds on Sassy, the approximate-DNA-searching tool that @rickbitloo.bsky.social and myself developed earlier this year, specifically with this application in mind.

Rick Beeloo@rickbitloo.bsky.social

Around 10% of your Nanopore reads (SQK-RBK114) are incorrectly trimmed. Here is why, and how our new tool Barbell solves it: www.biorxiv.org/content/10.1... Want to get started? github.com/rickbeeloo/b...

15 reposts20 likes

Ragnar {Groot Koerkamp}
@curiouscoding.nl

Barbell takes a principled approach to demultiplexing, and finds many more occurrences of barcodes/tags than e.g. Dorado does. Especially in cases where the tagging is messy (~8% of the reads), this avoids misclassification and bad trimming. And of course, cleaner data simplies downstreams tasks :)

Ragnar {Groot Koerkamp}
@curiouscoding.nl

Algorithmically, we first search for occurrences of <left-flank>NNNNNNN<right-flank> with up to 20 errors for rapid barcoding. Then, we match those against all <left-flank><barcode><right-flank> and assign the barcode with the minimal number of edits.

Ragnar {Groot Koerkamp}
@curiouscoding.nl

Since Sassy supports overhanging alignments, Barbell can also find partially clipped tags at the start/end of a read. In the end, we find that imprecise trimming results in barcodes making it into public assemblies, while re-assembling with Barbell-trimmed reads does not show such artifacts.