FormatRefDB | R Documentation |
Creates a reference database in UDB-format, which is compatible with the USEARCH function UTAX for taxonomic annotation. Optionally, the reference database can be restricted to gut-associated taxa, and/or only to named species.
FormatRefDB(refDB, usearch.path, confidence.file, gut.specific = F, taxman = F, named.species = F)
refDB |
The reference database in fasta format. This should either be the reference RDP database (http://drive5.com/usearch/manual/utax_downloads.html.) or a reference database from Taxman (http://www.ibi.vu.nl/programs/taxmanwww/). |
usearch.path |
Directory of the USEARCH program. |
confidence.file |
Taxonomy confidence file, which comes with the RDP reference data files at http://drive5.com/usearch/manual/utax_downloads.html. Select a suitable confidence file for your readlength. |
gut.specific |
TRUE if you want a gut-specific database. |
taxman |
TRUE if your database is from Taxman. |
named.species |
TRUE if you want to restrict the database to named species. |
Katri Korpela
Edgar, R.C. (2013) UPARSE: Highly accurate OTU sequences from microbial amplicon reads, Nature Methods [Pubmed:23955772,?? dx.doi.org/10.1038/nmeth.2604].
Brandt, B.W., Bonder, M.J., Huse, S.M. and Zaura, E. (2012) TaxMan: a server to trim rRNA reference databases and inspect taxonomic coverage. Nucleic Acids Research 40:W82-W87.
## Not run: #Create a gut-specific RDP reference database in UBD-format FormatRefDB(refDB = '/path/to/the/RDPreferencedatabase/from/UTAXdownloads/at/drive5.com', usearch.path = 'path/to/USEARCH8', confidence.file = '/path/to/the/taxonomicconfidencefile/from/UTAXdownloads/at/drive5.com', gut.specific = T) ## End(Not run)
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