igblastr

igblastr is an R/Bioconductor package that provides functions to conveniently install and use a local IgBLAST installation from within R.

To cite the igblastr package in publications, please use:

Pagès H, Hyrien O, MacPhee K, Duff M, Taylor J (2025). igblastr: User-friendly R Wrapper to IgBLAST. doi:10.18129/B9.bioc.igblastr https://doi.org/10.18129/B9.bioc.igblastr. https://bioconductor.org/packages/igblastr.

A BibTeX entry for LaTeX users is

@Manual{,
  title = {igblastr: User-friendly R Wrapper to IgBLAST},
  author = {Hervé Pagès and Ollivier Hyrien and Kellie MacPhee and Michael Duff and Jason Taylor},
  year = {2025},
  doi = {10.18129/B9.bioc.igblastr},
  url = {https://bioconductor.org/packages/igblastr},
}

Please also cite the original IgBLAST tool if you use it in your analysis.

See https://bioconductor.org/packages/igblastr for more information, including for how to install the release version of the package (please refrain from installing directly from GitHub).

BioC version	Status
release
devel

IgBLAST is described at https://pubmed.ncbi.nlm.nih.gov/23671333/

IgBLAST web interface: https://www.ncbi.nlm.nih.gov/igblast/

Please use https://github.com/HyrienLab/igblastr/issues to report bugs, provide feedback, request features, etc...

Quick start

1. Install and load igblastr

Install igblastr

First install and load BiocManager:

if (!require("BiocManager", quietly=TRUE))
    install.packages("BiocManager")

library(BiocManager)

Loading BiocManager should display a message that indicates the version of Bioconductor that you are using.

If you are using Bioconductor >= 3.22, simply install igblastr with:

BiocManager::install("igblastr")

This will install the version of igblastr that matches your version of Bioconductor.

If you are using Bioconductor 3.21, then you need to install directly from GitHub (usually discouraged). That's because igblastr was only added to Bioconductor >= 3.22 so cannot be installed from the Bioconductor 3.21 repositories:

if (!require("remotes", quietly=TRUE))
    BiocManager::install("remotes")

BiocManager::install("HyrienLab/igblastr")

Load igblastr

library(igblastr)

2. Set up IgBLAST

Install a pre-compiled IgBLAST

install_igblast()

This will download the arch-specific pre-compiled IgBLAST from https://ftp.ncbi.nih.gov/blast/executables/igblast/release/LATEST/ and install it in a persistent location. See ?install_igblast.

or use an existing installation of IgBLAST

Sys.setenv(IGBLAST_ROOT="path/to/igblast/root")

Note: Environment variable IGBLAST_ROOT should preferrably be set in a more persistent manner outside R e.g. by defining it in the user's .profile (on Unix/Mac). See ?IGBLAST_ROOT.

Check IgBLAST

igblast_info()

This will make sure that the installed IgBLAST is functional. It will also display basic information about it (e.g. igblastn version).

3. Install germline dbs and select db to use

Install germline dbs

At least one germline db must be installed.

Several specialized functions will be provided for that e.g.:

install_IMGT_germline_db()  # see '?install_IMGT_germline_db'
install_AIRR_germline_db()  # not ready yet!
# etc...

Select the germline db to use with igblastn()

list_germline_dbs()
use_germline_db(<db-name>)

See ?use_germline_db.

4. Select constant region db (optional)

The C-regions from IMGT are pre-installed for a few organisms:

list_c_region_dbs()

Select the C-region db to use with igblastn():

use_c_region_db(<db-name>)

See ?use_c_region_db.

5. Use igblastn()

See ?igblastn.