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

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

Online IgBLAST: 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

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

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.