How to demultiplex NGS data with custom barcodes from fastq files?

Question

[missTique]

I found a service that will sequence amplicons for cheap using Illumina 2x150. To lower the costs I want to multiplex samples using custom 9nt barcodes that I just tag to the 5' end of the amplicon forward primer. The service will not demultiplex samples for me, so I will be provided just the fastq files with all of the pooled sequences. I am wondering what is the most up to date and efficient method for demultiplexing custom barcodes from fastq files is?

Answer 1

[GenoMax]

If you know all the index combinations then you can use demuxbyname.sh from BBMap suite or deML package (A: Demultiplexing Illumina data ).