# igblastr [<img src="https://bioconductor.org/images/logo/jpg/bioconductor_logo_rgb.jpg" width="200" align="right"/>](https://bioconductor.org/)
[](https://bioconductor.org/packages/igblastr)
[](https://bioconductor.org/packages/stats/bioc/igblastr)
**igblastr** is an R/Bioconductor package that provides functions to conveniently install and use a local IgBLAST installation from within R.
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|
|------------|------|
| devel | [](https://bioconductor.org/checkResults/devel/bioc-LATEST/igblastr/) [](https://bioconductor.org/packages/devel/igblastr#since) |
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
First install and load **BiocManager**:
```r
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:
```r
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:
```r
if (!require("remotes", quietly=TRUE))
BiocManager::install("remotes")
BiocManager::install("HyrienLab/igblastr")
```
#### Load igblastr
```r
library(igblastr)
```
### 2. Set up IgBLAST
#### Install a pre-compiled IgBLAST
```r
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
```r
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
```r
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.:
```r
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()
```r
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:
```r
list_c_region_dbs()
```
Select the C-region db to use with `igblastn()`:
```r
use_c_region_db(<db-name>)
```
See `?use_c_region_db`.
### 5. Use igblastn()
See `?igblastn`.
