Install vtamR and Third Party Programs

Implementation

The heavy lifting of sequence analyses are done by the following third party programs. They should be installed on your computer:

• BLAST(Altschul et al., 1990) (v2.11.0+)
• vsearch (Rognes et al., 2016) (v2.7.0)
• cutadapt(Martin, 2011) (v4.0)
• swarm (Mahé et al., 2015) (v2.1.12)

vtamR has been tested using the above mentioned versions, but it should work with later versions. vtamR was tested on Windows and Linux, and should work in all operating systems.

• Help is available for all vtamR functions via ?function_name.
• Most functions accept either a data frame or a CSV file as input, and return a data frame (optionally saved to a CSV file if a filename is provided).

Install vtamR

pkg_install will handle conveniently the R dependencies of vtamR.

if(!requireNamespace("pak", quietly = TRUE)) install.packages("pak")
pak::pkg_install("meglecz/vtamR@develop")

Read the Manual on how to construct a full metabarcoding pipeline.

Install third party programs

Option 1: Install third party programs using conda environment

In R, find the full path to the YAML environment file:

environment_vtamR_yml_path <- system.file("environment_vtamR.yml", package = "vtamR")
cat(environment_vtamR_yml_path)

In a terminal, replace PATH_TO_YML with the path you just printed:

conda env create -f PATH_TO_YML
conda activate vtamRenv

This creates a Conda environment vtamRenv with all required tools.

If using RStudio, you must manually set the paths to these tools in your R session or scripts. See the Set up section of the tutorial for details.

Get paths to third-party programs:

conda activate vtamRenv

which vsearch
which blastn
which cutadapt
which swarm

Option 2: Install third party programs manually

Linux

• vsearch https://github.com/torognes/vsearch
• BLAST https://www.ncbi.nlm.nih.gov/books/NBK52640/
• cutadapt https://cutadapt.readthedocs.io/en/stable/installation.html
• swarm https://github.com/torognes/swarm

Windows

Download binaries and save it a convenient place on your computer (path without space, e.g. C:/Users/Public/)

vsearch

• Download binaries from https://github.com/torognes/vsearch/releases/tag/v2.23.0
• Decompress the zip file
• The executable are found in vsearch-x.xx.x-win-x86_64/bin/

cutadapt

• Download cutadapt.exe from https://github.com/marcelm/cutadapt/releases

swarm

• Download binaries from https://github.com/torognes/swarm/releases
• Decompress the zip file
• The executable is in the swarm-x.x.x-win-x86_64/bin directory

BLAST

• Detailed instructions: https://www.ncbi.nlm.nih.gov/books/NBK52637/
• Download executable (ncbi-blast-x.xx.x+-win64.exe) from https://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/
• Double click on the .exe file, accept the license agreement and specify the install location when prompted. Attention! Do not accept the standard location (C:/Program Files/…) since it contains a space. Chose a directory with a path without space (e.g. C:/Users/Public/).
• The executable are found in blast-x.xx.x+/bin/

TaxAssign reference data base

A ready-to-use COI database is available from OSF OSF, (Meglécz, 2023).

Download and extract using:

download_db(filename = "COInr_for_vtam_2025_05_23_dbV5.tar.gz",
    url = "https://osf.io/download/jyhz6/",
    dest_dir = "COInr_db",
    untar = TRUE,
    quiet = FALSE
    )

To check for newer versions:

• Go to: https://osf.io/vrfwz/files/osfstorage
• Navigate to the dbV5 folder.
• Choose your version → Click on the tree-dot menu → Right-click Download → Copy Link Address.

Alternatively, you can also create a custom version from the TSV format database available at Zenodo and make a custom version using mkCOInr (Meglécz, 2023).

For other markers you will need a database formatted to BLAST, containing taxIDs and a taxonomy file. If all sequences are extracted from NCBI-nt. The taxonomy file provided in OSF can be used without modification.