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QIIME 2

QIIME (Quantitative Insights Into Microbial Ecology) is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data. Since QIIME 1 is no longer supported officially (see announcement at http://qiime.org, it's not installed on the CentOS 7 system of HPCC. The way QIIME 2 is installed and run on the HPCC CentOS 7 is through conda https://docs.qiime2.org/2018.2/install/native/.

You may follow https://docs.anaconda.com/anaconda/install/linux to install anaconda in your home directory.

Below is how to install QIIME 2 (version 2018.2) in your home directory via conda:

Install QIIME 2

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export PATH=$PATH:$HOME/anaconda3/bin
wget https://data.qiime2.org/distro/core/qiime2-2018.2-py35-linux-conda.yml
conda env create -n qiime2-2018.2 --file qiime2-2018.2-py35-linux-conda.yml
rm qiime2-2018.2-py35-linux-conda.yml

source activate qiime2-2018.2
qiime --help # test if installation is successful
# all your QIIME commands go here
source deactivate

The example below is from a previous version of the current tutorial

Example of analysis

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mkdir qiime2-moving-pictures-tutorial
cd qiime2-moving-pictures-tutorial
wget -O "sample-metadata.tsv" "https://data.qiime2.org/2018.2/tutorials/moving-pictures/sample_metadata.tsv"

mkdir emp-single-end-sequences
wget -O "emp-single-end-sequences/barcodes.fastq.gz" "https://data.qiime2.org/2018.2/tutorials/moving-pictures/emp-single-end-sequences/barcodes.fastq.gz"
wget -O "emp-single-end-sequences/sequences.fastq.gz" "https://data.qiime2.org/2018.2/tutorials/moving-pictures/emp-single-end-sequences/sequences.fastq.gz"

qiime tools import \
  --type EMPSingleEndSequences \
  --input-path emp-single-end-sequences \
  --output-path emp-single-end-sequences.qza

qiime demux emp-single \
  --i-seqs emp-single-end-sequences.qza \
  --m-barcodes-file sample-metadata.tsv \
  --m-barcodes-column BarcodeSequence \
  --o-per-sample-sequences demux.qza

qiime demux summarize \
  --i-data demux.qza \
  --o-visualization demux.qzv

qiime tools view demux.qzv