How do i assign Fungal Taxon ID to ITS sequences?

11 November 2019 1 6K Report

I would like to assign taxon IDs to ITS amplicon sequences obtained using ITS 1 and ITS 4 primers. What would be the best program to use to get the nearest neighbors from the genebank?

Rodrigo Pereira

667/5000

There are many options for identifying fungal taxonomy by ITS. Some are: Use UNite database tools: https://unite.ut.ee/ Use classifier or sequence mate within rdp database https://rdp.cme.msu.edu/ with care to use ITS training set

An alternative to local analysis is PIPTS (https://sourceforge.net/projects/pipits/) information in the article https://doi.org/10.1111/2041-210X.12399 Other local alternatives are the famous Qiime (https://qiime2.org/) and clovr-ITS (https://microbiomejournal.biomedcentral.com/articles/10.1186/2049-2618-1-6). There are still many other options, but these above should already be of some help.

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