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

This software can be installed in your home directory using conda. It is not possible to install this software using pip at this time.

Installation Instructions

Instructions for installing QIIME 2 are provided by the developers are found here. These instructions, adapted for Compute Canada systems, are given below for version 2019.7. If a new version of the .yml file is released (check the link), use the newer version by updating the instructions below.

eb Miniconda3-4.5.12.eb
module load miniconda3
conda update conda
wget https://data.qiime2.org/distro/core/qiime2-2019.7-py36-linux-conda.yml
conda env create -n qiime2-2019.7 --file qiime2-2019.7-py36-linux-conda.yml
conda init bash
conda activate qiime2-2019.7

Remember to log out and back in after "conda init bash" step.

To use after installation, run:

module load miniconda3
conda activate qiime2-2019.7

External Sources

PANDAseq Assembler GitHub Repository
QIIME homepage
USEARCH homepage