QIIME

Qiime, PANDAseq & USearch

QIIME (canonically pronounced chime) stands for Quantitative Insights Into Microbial Ecology, is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data. QIIME is designed to take users from raw sequencing data generated on the Illumina or other platforms through publication quality graphics and statistics. This includes demultiplexing and quality filtering, OTU picking, taxonomic assignment, and phylogenetic reconstruction, and diversity analyses and visualizations. QIIME has been applied to studies based on billions of sequences from tens of thousands of samples.

PANDAseq assembles Illumina Solexa overlapping pair-end reads.

USEARCH is a unique sequence analysis tool with thousands of users world-wide. USEARCH offers search and clustering algorithms that are often orders of magnitude faster than BLAST.

Usage on new Compute Canada clusters

This software can be installed in your home directory on Graham by following the instructions provided by the qiime developers.

Installation Instructions

Instructions are provided by the developers found [here]. They are repeated below for convenience.

wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh 
chmod 700 Miniconda3-latest-Linux-x86_64.sh 
./Miniconda3-latest-Linux-x86_64.sh 
conda update conda 
conda install wget 
wget https://data.qiime2.org/distro/core/qiime2-2018.4-py35-linux-conda.yml 
conda env create -n qiime2-2018.4 --file qiime2-2018.4-py35-linux-conda.yml 
source activate qiime2-2018.4 
qiime --help 
rm Miniconda3-latest-Linux-x86_64.sh 
rm qiime2-2018.4-py35-linux-conda.yml

External Sources

PANDAseq Assembler GitHub Repository
QIIME homepage
USEARCH homepage