A universal parameter object for Bowtie 2 metagenomic or non-16S alignment
Source:R/data.R
bt2_regular_params.RdThis character string provides several Bowtie 2 options to provide a 95
alignment useful for metagenomes. 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_regular_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,0,1.7".
Further delineation of Bowtie 2 parameters is provided in the Bowtie 2 manual.
Examples
data("bt2_regular_params")