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 (use --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 (don't use --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 (don't use --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.