Fungal ITS Support

Feature requests
1

Dear Mothur Developers:

It would be nice if Mothur had some support for processing Fungal ITS sequences. I rely heavily on Mothur for my bacterial analysis, but I have to use on several outside programs to do any sort of Fungal ITS analysis, and even then it’s only basic analysis. It would help if there were a handful of features within Mothur to do a little of this analysis. Here are some of the requests:

  1. A way to incorporate cd-hit or a similar clustering method to assemble sequences into OTU’s without needing an alignment, or a way to build a list file from cd-hit outputs that will work within Mothur. I have a script I received from another researcher that can build a useable list file (so I can do some alpha and beta diversity analysis), but it’s cumbersome and sometimes doesn’t format well.

  2. A way to build some sort of matrix file from a list file. This would be the opposite of the cluster command. I’ve read a research paper that mentioned a script which could take a cd-hit output file and build a “OTU-distribution matrix”. I don’t have access to this script, but something like that could help.

  3. A way to get taxonomy data from ITS sequences. I know Mothur works primarily on sequence alignments, which aren’t possible with Fungal ITS data, but it would be nice to get some idea of taxonomy. I use a local install of NCBI blast with a database built by the UNITE public sequences, but it’s cumbersome and I don’t fully trust the results. I don’t know if this is possible within Mothur, but I thought I’d request it.

  4. A reliable chimera screening method for ITS data. I’ve used the chimera.uchime command using the data set as a template, but it only finds a handful of chimeras, so I don’t really trust it.

These are the three things I can think of off the top of my head, but any Fungal ITS support within Mothur would be nice and improve the functionality of the program. Thanks for the consideration.

Regards,

-Damon

2

Thanks for the suggestions - we’ll keep them in mind.

  1. A way to get taxonomy data from ITS sequences. I know Mothur works primarily on sequence alignments, which aren’t possible with Fungal ITS data, but it would be nice to get some idea of taxonomy. I use a local install of NCBI blast with a database built by the UNITE public sequences, but it’s cumbersome and I don’t fully trust the results. I don’t know if this is possible within Mothur, but I thought I’d request it.

You don’t need an alignment to do classification in mothur. You really just need a fasta file of ITS sequences and a file that contains their taxonomies. You might look at the 16S training sets to see how this is done.