Demultiplexing multiple amplicons from one fastq based on primer sequence

Question

[WhiteN8]

Hi all,

I have some fastq files that are already demultiplexed based on sample ID. I have separate fastq files for Read 1 and Read 2 per sample, from Illumina paired-end sequencing.

Within each sample fastq file, there are a mix of amplicons (~190). I need to demultiplex each file again, based on the primer sequences used to generate each amplicon.

Ideally I would end up with 190 files per sample fastq, each named with the Sample ID and the Primer ID for amplicon identification. I'd also like to output any reads that didn't match a primer sequence into some sort of unmatched file.

Any ideas on tools that could help me achieve this?

Many thanks in advance!

[Arup Ghosh]

Try Qiime split_libraries.py .

[WhiteN8]

Thanks for your suggestion - I can see split_libraries requires a mapping file with both barcode ID and primer sequence. I don't have the barcode sequence as it was removed in initial demultiplexing. Any idea if I can leave that blank?

[Arup Ghosh]

Demultiplexing will only remove the index adapter sequences, not the barcodes.

[charbelelias30]

Hello, did you finally succeed to do it? If yes how? I'm currently facing the same issue, I need to demultiplex each file again, based on the primer sequences to sort my data into ITS1 and ITS2. Any idea how I can do it using either qiime 2 or some other tool?

[Arup Ghosh]

Please start a new thread with more details.