bt2_regular_params: A universal parameter object for Bowtie 2 metagenomic or...
In compbiomed/MetaScope: Tools and functions for preprocessing 16S and metagenomic sequencing microbiome data
bt2_regular_params R Documentation
A universal parameter object for Bowtie 2 metagenomic or non-16S alignment
Description
This 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)
Format
list
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")
compbiomed/MetaScope documentation built on Nov. 20, 2024, 8 p.m.
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| bt2_regular_params | R Documentation |
A universal parameter object for Bowtie 2 metagenomic or non-16S alignment
Description
This 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)
Format
list
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")
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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