This pipeline is for analysis of 16s rRNA

This pipeline performs the following in order:

1. Quality check of raw reads
2. Trimming of adapters from reads
3. Merging/Stitching
4. Filtering and Primer removal
5. Orientation
6. Dereplication
7. Chimera detection
8. Clustering OTUs
9. Phylogeny
10. Taxonomy
11. Alpha diversity and Beta diversity

1. Install Nextflow(>21.11.3)
2. Install Trimmomatic(>V0.39), qiime2(>V2020.6), multiqc(>V1.4), vsearch(>V2.16.0)
3. Download the pipeline into your directory with the command

   git clone [email protected]:mbbu/16S_Accreditation.git
   

4. Test on the given test data with the command

   nextflow -C test.config run main.nf
   

5. Start running your own analysis

   nextflow run main.nf --primers primers.txt --metadata metadata.tsv --reads microbiome-data/*_R{1,2}.fastq.gz
   

Check this contributors page for collaborators. All are listed in the report, including those who did not commit to GitHub.