LEfSe (Linear discriminant analysis Effect Size) determines the features (organisms, clades, operational taxonomic units, genes, or functions) most likely to explain differences between classes by coupling standard tests for statistical significance with additional tests encoding biological consistency and effect relevance.
LEfSe is available as a Galaxy module, a Homebrew formula, a Docker image, and included in bioBakery (VM and cloud). For additional information, please refer to the LEfSe paper.
We provide support for LEfSe users. Please join our Google group designated specifically for LEfSe users. Feel free to post any questions on the google group by posting directly or emailing lefse-users@googlegroups.com.
For the purpose of this tutorial we will be using a sample input file (hmp_small_aerobiosis.txt).
You may also plot differential features or one feature. Please refer to the LEfSe documentation for more information.
LEfSe can be installed with Homebrew or run from a Docker image. Please note, if you are using bioBakery (Vagrant VM or cloud) you do not need to install LEfSe because the tool and its dependencies are already installed.
Install with Homebrew: $ brew install biobakery/biobakery/lefse
Install with Docker: $ docker run -it biobakery/lefse bash
If you would like to install from source, refer to the LEfSe documentation (Step 4).
For the purpose of this tutorial we will be using a sample input file: hmp_small_aerobiosis.txt depicting the general format of the input file (two rows of metadata, one row of sample names and the corresponding microbial abundance table).
To visualize the results, LEfSe provides a couple of options. For all the options you will need the output from run_lefse.py (in this case: hmp_aerobiosis_small.res)
For information on more options, and further analyses, please refer to Step 4 in the MetaPhlAn Pipeline Tutorials.
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