Microbiome analysis using QIIME
Bioinformatics Core Facility
National Institute of Biotechnology in the Negev, Ben Gurion University.
Developed as part of a study led by Prof. Jacob Moran-Gilad.
- Read preparation:
trimmomatic - For cleaning the reads
FastQC - Checking the quality of the reads
Optional read joining with join_paired_ends.py (module
Creating symbolic links to files so that demultiplication can recognise the sample names from the link names.
Further QA and concatenating all sequences into a single fasta file with
Identifying chimeric sequences (
- Analysis (denovo OTU picking)
selecting representative sequences
Aligning to reference and filtering the alignment
Assigning taxonomic lineage to representative sequences
Creating phylogenetic tree
Creating BIOM table
Computing core diversity analyses on the BIOM table.
You can filter out particular samples or OTUs with modules
You can sort the BIOM table samples by a specific field of the mapping file with the
fastq files. Paired end or single-end.
#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