I’m using mothur (v.1.36.1) from Galaxy and would like to know what a tool is exactly doing. From the logs I can see that the following command is executed
I have read the wiki for the command, but it seems that there are quite some gaps in the explanations. Is there any other information source? Unfortunately I could not search the forum – because there is no search function (see https://github.com/mothur/mothur/issues/372).
Thanks a lot.
First, please update to 1.39.5. You do not have the latest clustering algorithm if you are using 1.36. We don’t have any interaction with the galaxy people, so I’m not sure what their plans are for upgrading tools. Second, if you have questions about a specific algorithm that we created, you can often find a paper describing it in Pubmed.
You can read more about cluster.split in ( run: cluster.split(citation) )…
Schloss PD, Westcott SL (2011). Assessing and improving methods used in OTU-based approaches for 16S rRNA gene sequence analysis. Appl Environ Microbiol 77:3219.
The new clustering algorithm is described in
Westcott SL, Schloss PD. 2017. OptiClust, an Improved Method for Assigning Amplicon-Based Sequence Data to Operational Taxonomic Units. mSphere. 2: e00073-17
Hope these help, but definitely update your version of mothur.
Thanks a lot. This helps me to find the required documentation.
I heard that the galaxy people are currently working on an update, but this might need a while.