This character string provides several Bowtie 2 options to provide an
optimized alignment specifically optimized for 16S amplicon sequencing data.
This object can be used with functions that use the Bowtie 2 aligner through
the Rbowtie2 package, namely align_target_bowtie() and
filter_host_bowtie. These settings can be substituted for default
settings by passing to the bowtie2_options argument.
Usage
data(bt2_16S_params)Details
The default parameters listed in this object are "--local -R 2 -N 0 -L 25 -i S,1,0.75 -k 5 --score-min L,0,1.88"
Note that k is actually 10 and is doubled internally from 5.
The score-min function was chosen such that the minimum alignment score
allowed requires 98
Further delineation of Bowtie 2 parameters is provided in the Bowtie 2 manual.
Examples
data("bt2_16S_params")