How do I import my .qz files from illumina sequencing into qiime2 via a manifest file?

Question

My data is from 16S gene sequencing that went through illumina and it is paired-end, demultiplexed, and does NOT have barcodes. I went through the qiime2 importing guide and it looks like I have to make a manifest file and I am not sure how to do so. My data is structured as some control_1_R1.fq, Control_1_R2.fq, control_2_R1.fq, Control_2_R2.fq, Data_3_R1.fq, Data_3_R2.fq,Data_4_R1.fq, Data_4_R2.fq.fq...etc. If the answer is not to make a manifest file then how else can I turn these.fq demultiplexed paired end sequences into qza files for qiime2?

Answer 1

fastq.gz files look like

1. The software edition I used is: Qiime2 2021.4

2. The file type is same as yours: paired-end demultiplexed fastq

3. /data is the name of the folder where all the paired end reads files are located.

4. The code you should run in your terminal is: qiime tools import --type 'SampleData[PairedEndSequencesWithQuality]' --input-path /data --input-format CasavaOneEightSingleLanePerSampleDirFmt --output-path demux.qza

5. You don't have to have a manifest file, but you need to have a metadata file which contains a column called Sample_ID, usually it should be the first column in the metadata.tsv or metadata.txt file. the metadata file looks like this: https://docs.google.com/spreadsheets/d/1i-0SrMP5D3-nMgnoKeP8VVvpp_aGE15-l7n5W5tiqPY/edit#gid=0