bt2_16S_params: A universal parameter object for Bowtie 2 16S alignment

In compbiomed/MetaScope: Tools and functions for preprocessing 16S and metagenomic sequencing microbiome data

A universal parameter object for Bowtie 2 16S alignment

Description

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)

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,0,1.88"

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")

compbiomed/MetaScope documentation built on April 1, 2024, 5:35 p.m.