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

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. 30, 2024, 4:35 p.m.