FormatRefDB: Create a UDB-format reference database

In katrikorpela/mare: Microbiota Analysis in R Easily

Create a UDB-format reference database

Description

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.

Usage

FormatRefDB(refDB, usearch.path, confidence.file, gut.specific = F, 
    taxman = F, named.species = F)

Arguments

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.

Author(s)

Katri Korpela

References

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.

Examples

	## 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)

katrikorpela/mare documentation built on July 17, 2022, 2:49 a.m.