Installing QIIME1

See the QIIME Installation Guide for easy installation of QIIME1 using Conda in Mac and Linux environments.

Split libraries

split_libraries_fastq.py – This script performs demultiplexing of fastq sequence data where barcodes and sequences are contained in two separate fastq files (common on Illumina runs).

The following parameters have been tested with typical Illumina fastq output:

# 16S (with --rev_comp_barcode)
split_libraries_fastq.py 
    -i 16S_data_S1_L001_R1_001.fastq.gz 
    -b 16S_data_S1_L001_I1_001.fastq.gz 
    --rev_comp_barcode 
    --rev_comp_mapping_barcodes 
    -o /path/to/outputdir 
    -m /path/to/map.txt 
    -q 19

# 18S (NO --rev_comp_barcode)
split_libraries_fastq.py 
    -i 18S_data_S1_L001_R1_001.fastq.gz 
    -b 18S_data_S1_L001_I1_001.fastq.gz 
    --rev_comp_mapping_barcodes 
    -o /path/to/outputdir 
    -m /path/to/map.txt 
    -q 19

# ITS (NO --rev_comp_barcode)
split_libraries_fastq.py 
    -i ITS_data_S1_L001_R1_001.fastq.gz 
    -b ITS_data_S1_L001_I1_001.fastq.gz 
    --rev_comp_mapping_barcodes 
    -o /path/to/outputdir 
    -m /path/to/map.txt 
    -q 19

Pick OTUs

pick_closed_reference_otus.py – Closed-reference OTU picking, e.g. using Greengenes 97% OTUs.

pick_closed_reference_otus.py 
    -i /path/to/seqs.fna 
    -r /path/to/97_otus.fasta 
    -t /path/to/97_otu_taxonomy.txt 
    -o /path/to/otus_closed_ref_gg97

deblur workflow – De novo OTU picking. Deblur is a greedy deconvolution algorithm based on Illumina MiSeq/HiSeq error profiles.

deblur workflow 
    --seqs-fp /path/to/seqs.fna 
    --output-dir /path/to/deblur_150bp 
    -t 150

Core diversity analyses

core_diversity_analyses.py – A workflow for running a core set of QIIME diversity analyses. Please also try the many individual scripts that this script wraps.

Continuing with QIIME…

For more information, please visit the websites for QIIME1 and QIIME2.