RasperGade16S: Prediction and correction of 16S rRNA GCN

RasperGade16S is a specialized R package that predicts the 16S rRNA GCN of bacteria given their 16S rRNA gene sequence.

In addition to what RasperGade can do, RasperGade16S has some functions dedicated to 16S rRNA GCN:

1. addressing rate heterogeneity with a binary rate model

2. providing an established pipeline to predict 16S rRNA GCN

3. correcting 16S rRNA GCN variation in analyses of bacterial composition with confidence provided

Detailed analyses are described in the paper: Accounting for 16S rRNA copy number prediction uncertainty and its implications in microbial diversity analyses

doi: (https://doi.org/10.1038/s43705-023-00266-0)

System requirements

For full functionality of RasperGade16S, POSIX-compliant system (e.g., Linux or macOS but not Windows) is required.

The package has been tested on Ubuntu and macOS.

The following software is required:

HMMER 3 (available from http://hmmer.org/)

EPA-ng (available from https://github.com/Pbdas/epa-ng)

You can download the raspergade13.yml file and use conda (https://www.anaconda.com) to install HMMER3 and EPA-ng.

    conda env create -f raspergade16s.yml

For macOS, you can install HMMER3 and EPA-ng using brew (https://brew.sh)

    brew install hmmer
    brew install easel
    brew install epa-ng

The following R packages are required: ape,castor,RasperGade,phyloseq,vegan,seqinr,treeio,microbiome

Installation

RasperGade and RasperGade16S can be installed using the following command in R

if (!requireNamespace("devtools", quietly = TRUE))
    install.packages("devtools")
devtools::install_github(repo = "wu-lab-uva/RasperGade")
devtools::install_github(repo = "wu-lab-uva/RasperGade16S")

treeio,phyloseq,microbiome can be installed from Bioconductor

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("phyloseq")
BiocManager::install("treeio")
BiocManager::install("microbiome")

Other packages can be installed from CRAN

install.packages("ape")
install.packages("castor")
install.packages("vegan")
install.packages("seqinr")

Data format

RasperGade16S can start from 16S rRNA sequences (e.g., representative sequences for OTUs)

Demo

Once installed, a small demo can be run in R to check if RasperGade16S operates properly:

library(RasperGade16S)
pred.GCN = predict_16SGCN_from_sequences()
print(pred.GCN$tab)

If everything works well, the following output should be expected

              label x      probs
0.1 GY203941.1.1493 4 0.99999796
0.2 GY324971.1.1500 9 0.82278712
0.3 JQ765433.1.1505 8 0.04355867
0.4 JQ765578.1.1444 6 0.83112359
0.5 JQ766308.1.1248 2 0.99966469

To run on your own sequence, supply the path to the FASTA file via the seqs= argument

pred.GCN = predict_16SGCN_from_sequences(seqs=PATH_TO_YOUR_SEQUENCE)