Demultiplex nanopore reads with custom barcodes We have a problem trying to demultiplex MinION sequences with custom barcodes. Do you have any software recommendations we can try for demultiplexing or how to demultiplex these custom barcodes with Albacore? We have tried using albacore but it only recognizes barcodes provided by Nanopore Technologies.
My semi-automatic workflow for demultiplexing nanopore reads using LAST can be found here - pay attention to the comments, where I've identified bits in the steps which might trip up people trying to follow them:

https://dx.doi.org/10.17504/protocols.io.7vmhn46

While this protocol is designed around using the ONT barcodes, the barcode fasta file can be replaced by another file [using barcode ID in the header] without changing the protocol. Make sure that this file only includes the unique parts of the barcodes (with a few bases of context if necessary to exclude random matches), so that reads won't be matched to the non-unique part of the wrong barcode sequence.