databases.rst

Supported databases

16S rRNA

• Greengenes ftp://greengenes.microbio.me/greengenes_release/
• Greengenes Core Set (useful for NAST) http://greengenes.lbl.gov/Download/Sequence_Data/Fasta_data_files/core_set_aligned.fasta.imputed
• QIIME-formatted SILVA https://www.arb-silva.de/download/archive/qiime/

ITS

• UNITE https://unite.ut.ee/repository.php (QIIME releases)

  Note

  In the QIIME releases of the UNITE database the _s in the filename (e.g. sh_qiime_release_s_DD.MM.YYY.zip) specifies that the database includes singletons.