QIIME

QIIME 1

update 2018: consider using the new version → QIIME 2

Tutorials QIIME 1

http://qiime.org/tutorials/index.html

http://www.wernerlab.org/teaching/qiime

https://github.com/alexcritschristoph/Qiime16sTutorial

https://sites.google.com/site/knightslabwiki/qiime-workflow

http://www.science.smith.edu/.../2015/Tutorial-to-analyzed-data-using-Qiime.pdf

https://twbattaglia.gitbooks.io/introduction-to-qiime/content/

Analysis Steps QIIME 1

→ Install QIIME 1

1) Sequence pre-processing

Sequence quality control, remove primer, and join forward and revers reads.

Result: seqs.fna (file containing all sequences)

2) OTU picking

Get → OTU cluster of similar sequences and select a reference sequence

Result: otu_table_mc2_w_tax.biom (OTU abundance table of all samples, including taxonomy)

3) Taxonomy

Which microbes are present and at which relative abundance?

Result: Taxa/taxa_summary_plots/bar_charts.html (to open in web-browser)

Taxa/otu_table_mc2_w_tax_no_pynast_failures_L6.txt (relative abundance taxa tables)

4) Statistical tests

Which microbes show the largest differences between environmental conditions?

Results: List of microbial taxa, ranked by p-values for statistical significance between the conditions.

5) Community stats: Alpha & Beta diversity

How different is the the microbial composition between samples?

Results: number of taxa per sample, PCoA plots