The bioBakery help forum

LefSe's example input file

I can not find LefSe’s example input file: hmp_small_aerobiosis.txt. The original link on bioBakery can not be found. Does anyone has a clue?

No idea, but, I would suggest to you to run it directly on your own input file - lefse format is pretty straight forward. These are the important points:
-default is feature names in rows, sample names in columns
-EVERY column must have a header (you can name the feature column with “Group” or something like that
-you can input between 1 to 3 header rows (for class, subclass, sample ID - the last two are optional)
-headers can have only letters,digits or underscore . No special characters or spacers!
-If you want LEfSe to treat feature names as heirarchial - for example, run comparisons at species level, genus level, et cetera - use “|” to denote levels. For example: Bacteria|Firmicutes|Clostridia|Clostridiales|Lachnospiraceae|Blautia
This is also necessary if you want it to output a meaningful cladogram

Hi -

Were you having troubles accessing the following link?

It worked okay for me. But we are going through a migration to GitHub so that might be causing issues. If the above link still does not work, could you try this new link at LefSe’s GitHub tutorial page?


Hi leahfa,

Thanks for the detailed info. I will have a try.