Quantitative Insights into Microbial Ecology (QIIME)

Illumina Overview Tutorial

Getting started

Downloading the tutorial data from ftp://ftp.microbio.me/qiime/tutorial_files/moving_pictures_tutorial-1.9.0.tgz

For the purpose of this tutorial we will be using the dataset available here: https://github.com/galaxyproject/tools-iuc/tree/qiime/tools/qiime/test-data

Check our mapping file for errors

validate_mapping_file.py – Checks user’s metadata mapping file for required data, valid format

Demultiplexing and quality filtering sequences

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).

!split_libraries_fastq.py -o slout/ -i forward_reads.fastq.gz -b barcodes.fastq.gz -m map.tsv

Input fastq files  forward_reads.fastq.gz Metadata mapping files (optional)  map.tsv Barcode read files (optional)  barcodes.fastq.gz

count_seqs.py –

!count_seqs.py -i slout/seqs.fna

Input sequence file  52 Split fastq libraries on data 18, data 11, and data 19: sequences

53 Count sequences on data 52: sequence counts

[http://nbviewer.jupyter.org/github/biocore/qiime/blob/1.9.1/examples/ipynb/illumina_overview_tutorial.ipynb#OTU-picking:-using-an-open-reference-OTU-picking-protocol-by-searching-reads-against-the-Greengenes-database. OTU picking: using an open-reference OTU picking protocol by searching reads against the Greengenes database.]

pick_open_reference_otus.py – Perform open-reference OTU picking

!pick_open_reference_otus.py -o otus/ -i slout/seqs.fna -p ../uc_fast_params.txt

Input sequence files  52 Split fastq libraries on data 18, data 11, and data 19: sequences

!biom summarize-table -i otus/otu_table_mc2_w_tax_no_pynast_failures.biom

Run diversity analyses

core_diversity_analyses.py – A workflow for running a core set of QIIME diversity analyses.

!core_diversity_analyses.py -o cdout/ -i otus/otu_table_mc2_w_tax_no_pynast_failures.biom -m map.tsv -t otus/rep_set.tre -e 1114

OTU table  123 Perform open-reference OTU picking on data 52: OTU table with taxonomy  # OR  122 Perform open-reference OTU picking on data 52: OTU table Mapping file  11 map.tsv Sequencing depth to use for even sub-sampling and maximum rarefaction depth  1114 Tree file  126 Perform open-reference OTU picking on data 52: representative set tree


179 Compute core set of diversity analyses on data 11 and data 123: Core diversity report

tool error An error occurred with this dataset:

cannot find ‘tree_fp’ while searching for ‘phylogenetic.tree_fp’



たたき台としてどのツールを使うか検討:このページ の QIIME in Galaxy

Pitagora 0.3.2 に Tool Shed の package_python_2_7_qiime_1_9_1 のインストール


$ sudo apt-get install pkgconfig

Pandas のインストールでエラーが出ている

'latin-1' codec can't encode character u'\u2018' in position 1794: ordinal not in range(256)