How to demultiplex NGS data with custom barcodes from fastq files?
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3.7 years ago
missTique • 0

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?

sequencing amplicon amp-seq ngs barcode • 2.9k views
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Entering edit mode
3.7 years ago
GenoMax 141k

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

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