16s analysis with QIIME2

Our fastq files are paired-end, demultiplexed and have the type PairedEndManifestPhred33V2. Your fastq files can have any format, just change the correspondig parameters at the input process. Due to company confidentiality I can't provide you the fastq files, but I am going to explain everything you need to run your own analysis!

About FASTQ files:

There are two fastq files for each sample in the study, each containing the forward or reverse reads for the sample, respectively. The names of the files should include the following information (For PairedEndManifestPhred33V2):

• Sample identifier

• Barcode sequence or a barcode identifier

• Lane number

• Direction of the read:

  R1 = Forward read
  R2 = Reverse read

• Set number

Example : A0C_S96_L001_R1_001.fastq and A0C_S96_L001_R2_001.fastq

The steps for our analysis are:

1. Import raw files into Qiime2

2. Use of DADA2 tool for:

   • Filtering

   • Dereplication

   • Chimera Identification

   • Merging paired-end reads

3. Taxonomic Analysis and some filtering

4. Phylogenetic tree

5. Rarefaction curves and calculation of Diversity metrics

For more informations dive into code (qiime2_commands.sh) and don't forget to read my comments (They are pretty helpful :) )