Where can I get reference databases for chimera filtering?

To use the chimera removal tool in Geneious R10, you must supply your own reference database.  This should be a sequence list of high-quality sequences believed to be free of chimeras, and include sequences that are likely to appear as parents in the query set.  It is recommended to use the largest possible database e.g. SILVA for 16S or UNITE for ITS.  

Silva: SILVA provides comprehensive, quality checked and regularly updated datasets of aligned small (16S/18S, SSU) and large subunit (23S/28S, LSU) ribosomal RNA (rRNA) sequences for all three domains of life (BacteriaArchaea and Eukarya).  FASTA files for Silva databases are available from here, and further information on the database contents is given here.

Fungal ITS: UNITE:  Currently this is the only recommended database for chimera detection in fungal ITS sequences. It includes datasets for each of full length ITS1 and ITS2.  To download, go to the UNITE Resources page.  Expand the UCHIME/USEARCH/UTAX reference datasets link and go to the List of all UCHIME reference datasets section, then click the Download link for your desired version. Extract the appropriate FASTA file from the zip archive, then import into Geneious as nucleotide sequences. Includes only forward strands.

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