I've got a fastq file containing multiplexed amplicon sequencing on ONT, so reads are unpaired and can be sense or antisense. The amplicons are asymmetrically barcoded, meaning distinct samples within the fastq file can be distinguished by the forward barcode at one end and the reverse barcode at the other. The structure of the amplicon is this:
pad - forward barcode - forward adapter - target sequence - reverse adapter - reverse barcode - pad
I've been playing around with cutadapt, but can only get it to demultiplex and name based on one barcode.
micromamba activate bioinfo
BARCODES="path/to/barcodes.fasta"
FASTQ="path/to/data.fastq"
OUT="path/to/temp"
cutadapt -e 0.1 \
-g file:"$BARCODES" \
-a file:"$BARCODES" \
-o "$OUT/demux-{name}.fastq" \
"$FASTQ" > "$OUT/cutadapt_log.txt"
Ultimately I'm hoping to get it to demultiplex using both F and R barcodes, e.g.: demux-fbc01-rbc01.fastq demux-fbc02-rbc01.fastq etc.
If it's possible to also trim off the barcodes, leaving the target sequence only, that would also be great.
Any help much appreciated!
