how to demultiplex when barcodes are inside the sequence?

i have 23 reads file in fastq format how could i remove barcode from the sequence/reads file

Try this: https://docs.qiime2.org/2019.10/plugins/available/cutadapt/

Are your data paired end, or single end? Where in the read is the barcode located?

Colin

the data is single end

and i have a barcode sequence which length is 10 bp and every sequence has unique barcode.

OK!

Does this mean you have 23 different barcodes and 23 different samples? One for each fastq file?

yes i have different barcodes for each samples.

as i got my file in sff format then which protocol i should go through casava or emp

If you have sff files, the first thing you should do is convert them into fastq files.

Do you have 23 separate fastq files?

If you already have separate fastq files, you should use the Fastq manifest format.

Colin