There are two IgBlast command line programs, igblastn and igblastp. The former is for nucleotide sequences and the latter is for protein sequences.

igblastn examples

Searching germline gene database

These examples assume that your current working directory has the following file structure:

igblastn
myseq
database
internal_data
optional_file 

Assuming you have put your germline gene blast database files under the directory “database”, to query one or more mouse Ig sequences (contained in myseq) against NCBI mouse germline gene database with standard text alignment result format, you can issue the following command:

 ./igblastn -germline_db_V database/mouse_gl_V -germline_db_J database/mouse_gl_J -germline_db_D database/mouse_gl_D -organism mouse -query myseq -auxiliary_data optional_file/mouse_gl.aux -show_translation -outfmt 3

To query human Ig sequences against IMGT germline database:

./igblastn -germline_db_V database/imgt.Homo_sapiens.V.f.orf -germline_db_J database/imgt.Homo_sapiens.J.f.orf -germline_db_D database/imgt.Homo_sapiens.D.f.orf -organism human -query myseq -auxiliary_data optional_file/human_gl.aux -show_translation

To query human Ig sequences against custom database (using IGH repertoire from Andew Collins et al as an example)

./igblastn -germline_db_V database/UNSWIgVRepertoire_fasta.txt -germline_db_J database/UNSWIgJRepertoire_fasta.txt -germline_db_D database/UNSWIgDRepertoire_fasta.txt -organism human -query myseq  -auxiliary_data optional_file/human_gl.aux -show_translation

To query mouse T cell receptor sequences against imgt mouse germline gene database:

./igblastn -germline_db_V database/imgt_tcr_db_v -germline_db_J database/imgt_tcr_db_j -germline_db_D database/imgt_tcr_db -organism mouse -query myseq -ig_seqtype TCR -auxiliary_data optional_file/mouse_gl.aux -show_translation -outfmt 3

you can type

./igblastn -help

to see details on all input parameters and the default setting, particularly those under Ig-BLAST options.

Searching other databases in addition to germline database.

Igblast allows you to search an additional database (such as NCBI nr database) as well as the germline database at the same time. You’ll get hits from the germline database followed by hits from the additional database. Note that the additional database may not contain any sequences identifiers that also exist in germline databases.

To query mouse Ig sequences against NCBI nr database, in addition to mouse germline database:

./igblastn -germline_db_V database/mouse_gl_V -germline_db_J database/mouse_gl_J -germline_db_D database/mouse_gl_D -organism mouse -query myseq -auxiliary_data optional_file/mouse_gl.aux -show_translation -outfmt 3 -db nr -remote 

Note the -remote option used with this search…it directs igblast to send nr database searching to NCBI server which typically is much faster.

igblastp examples:

The parameters are similar to those of igblastn except it does not search germline D database or germline J database. The optional file is not needed.
Some examples:

Searching mouse Ig sequence against mouse germline gene database
./igblastp -germline_db_V database/mouse_gl_V -query myseq.prot -outfmt 3 -organism mouse
Searching other databases in addition to germline database.
./igblastp -germline_db_V database/mouse_gl_V -query myseq.prot -outfmt 3 -organism mouse -db nr -remote