Your sequencing facility should have given you the demultiplexed data. If you have done if yourself you must need more information than just name of a tool for the purpose. Go through the info in following link.

https://bioinformatics.cvr.ac.uk/how-to-demultiplex-illumina-data-and-generate-fastq-files-using-bcl2fastq/

If you have file with barcodes and a metadata, you can use for demultiplexing:

1. Cutadapt

2. Sabre

Or, you can demultiplex fastq files and perform 16S analysis with Qiime2 or Mothur.

Hello Paulina,

if you need help for managing and interpret your 16S data, don't hesitate to contact us: [email protected]

We have performed several analysis on microbiota (Lamas et al., 2016. Nat. medecine, Lamas et al., 2018. Gut, Natividad et al., 2018. Nat. Communication)

Let me know.

Best