Microbiome analysis using QIIME


Menachem Sklarz


Bioinformatics Core Facility


National Institute of Biotechnology in the Negev, Ben Gurion University.

A workflow for executing a complete QIIME analysis (based on QIIME 1.9.. A new workflow for QIIME2 is also available)

Developed as part of a study led by Prof. Jacob Moran-Gilad.


  1. Read preparation:
    1. merge

    2. trimmomatic - For cleaning the reads

    3. FastQC - Checking the quality of the reads

    4. MultiQC

    5. Optional read joining with join_paired_ends.py (module qiime_prep)

    6. Creating symbolic links to files so that demultiplication can recognise the sample names from the link names.

    7. Further QA and concatenating all sequences into a single fasta file with qiime_demult.

    8. Identifying chimeric sequences (qiime_chimera module`)

  2. Analysis (denovo OTU picking)
    1. OTU picking

    2. selecting representative sequences

    3. Aligning to reference and filtering the alignment

    4. Assigning taxonomic lineage to representative sequences

    5. Creating phylogenetic tree

    6. Creating BIOM table

    7. Computing core diversity analyses on the BIOM table.

  3. Optional
    1. You can filter out particular samples or OTUs with modules qiime_filter_samples_from_otu_table and qiime_filter_otus, respectively.

    2. You can sort the BIOM table samples by a specific field of the mapping file with the qiime_sort_otu_table module

Workflow Schema

QIIME workflow DAG


fastq files. Paired end or single-end.

Programs required

Example of Sample File

Title       Metagenomics

#SampleID   Type    Path    lane
Sample1     Forward /path/to/Sample1_F1.fastq.gz 1
Sample1     Forward /path/to/Sample1_F2.fastq.gz 2
Sample1     Reverse /path/to/Sample1_R1.fastq.gz 1
Sample1     Reverse /path/to/Sample1_R2.fastq.gz 2
Sample2     Forward /path/to/Sample2_F1.fastq.gz 1
Sample2     Reverse /path/to/Sample2_R1.fastq.gz 1
Sample2     Forward /path/to/Sample2_F2.fastq.gz 2
Sample2     Reverse /path/to/Sample2_R2.fastq.gz 2


The workflow file is available here