This character string provides several Bowtie 2 options to provide a loose
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_loose_params)Details
The default parameters listed in this object are "--local -k 100 -D 20 -R 3 -L 3 -N 1 -p 8 --gbar 1 --mp 3".
Further delineation of Bowtie 2 parameters is provided in the Bowtie 2 manual.
These parameters were chosen from the article bowtie2: Relaxed Parameters for Generous Alignments to Metagenomes.
Examples
data("bt2_loose_params")