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...

For rapid barcoding only ~83% of the reads contain the expected single barcode on the left. The rest? Barcodes on both sides (6.1%), two barcodes on the left side (3.5%), and so on.

Many tools, including the widely used Dorado, almost always only detected the *first* occurrence, leaving the rest untrimmed. In the figure black lines indicate matches to adapters + barcodes in trimmed reads.

Why is this a problem? Remaining adapters/barcodes not only contaminated assemblies but also created "artificial" links in taxonomic annotation, to Enterobacteriaceae, and to contaminated assemblies in NCBI.

In Barbell we solve this by first annotating all the reads, and then detecting all patterns, which looks like this: