This pipeline uses QIIME 2 to import, quality control, denoise, assign taxonomy, and generate a taxonomic bar plot for paired-end sequencing data. The pipeline consists of the following steps:
1-> Import the paired-end FASTQ files into QIIME 2
2-> Perform quality control on the paired-end FASTQ files
3-> Denoise the paired-end sequences to generate feature tables and representative sequences
4-> Tabulate the representative sequences
5-> Assign taxonomy to the representative sequences using the SILVA database
6-> Review the taxonomy associated with the sequences
7-> Generate a taxonomic bar plot
- QIIME 2 (version 2021.2 or later)
- SILVA database (version 138 or later)
- Paired-end sequencing data in FASTQ format
To run the pipeline, execute the following command in the terminal:
bash pipeline.sh SEQ_DIR
where "SEQ_DIR" is the path to the directory containing the paired-end FASTQ files.
The pipeline generates the following outputs:
- paired-end-demux.qza: imported paired-end FASTQ files
- paired-end-demux-summary.qzv: quality control summary of the paired-end FASTQ files
- rep-seqs.qza: representative sequences of the denoised paired-end sequences
- table.qza: feature table generated from the denoised paired-end sequences
- denoising-stats.qza: denoising statistics generated during the denoising process
- rep-seqs.qzv: visualization of the representative sequences
- taxonomy.qza: taxonomic classification of the representative sequences
- taxonomy.qzv: visualization of the taxonomic classification
- taxa-bar-plots.qzv: taxonomic bar plot
The outputs are exported to the following directories:
- Export_1: exported rep-seqs.qzv
- Export_2: exported taxonomy.qzv
- Export_3: exported taxa-bar-plots.qzv
For more information about QIIME 2, please refer to the official documentation.