Simple: Pre-processing of raw 16S amplicon sequences and creation of...

In katrikorpela/mare: Microbiota Analysis in R Easily

Pre-processing of raw 16S amplicon sequences and creation of taxonomic tables in one simple function

Description

The function processes the forward reads. It trims the primer sequences and truncates the reads to 150 bases. The reads are dereplicated and rare reads (representing <0.1 percent of the reads) are removed. OTU clustering and taxonomic annotation of the reads is done using USEACH.

Usage

Simple(forward.reads = NULL, forward.primer = NULL, name.separator = "_", 
    folder.name = "", usearch.path, refDB)

Arguments

forward.reads	List of the forward reads.
forward.primer	Primer sequence to be removed from the forward reads.
name.separator	Character that separates the sample name in the beginning of the read files.
folder.name	Name for the new folder where the processed reads are written.
refDB	The reference database in fasta format, produced by FormatRefDB-function or from mare.
usearch.path	Directory of the USEARCH program.

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].

Examples

	## Not run: 

Simple(forward.reads = list.files(pattern = '_R1_'),
             usearch.path = 'path/to/USEARCH8',
             forward.primer = c('AAATCGTACG'),
             folder.name = 'Example')

## End(Not run)

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