Demultiplex nanopore reads with custom barcodes
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.