QIIME 1update 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://www.gitbook.com/book/twbattaglia/introduction-to-qiime/details
→ Install QIIME 1
Sequence quality control, remove primer, and join forward and revers reads.
Result:
seqs.fna (file containing all sequences)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)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)Which microbes show the largest differences between environmental conditions?
Results: List of microbial taxa, ranked by p-values for statistical significance between the conditions.
How different is the the microbial composition between samples?
Results: number of taxa per sample, PCoA plots |