Demultiplexing paired-end illumina data with separated R1 file, R2 file and index file

Question

[evg16]

I need help demultiplexing paired-end fastq files. I was given an index file, an R1 fastq, an R2 fastq, and the barcode spreadsheet. Is there any way to do this on R?

[swbarnes2]

What kind of lazy sequencing facility goes through the work of making your fastqs without demultiplexing for you?

Answer 1

[GenoMax]

Not in R but you could do this using a program called demuxbyname.sh in BBMap suite. See an example --> demuxbyname.sh output help

Other option would be to use a program like deML: https://github.com/grenaud/deML