igblast is a tool developed at NCBI for analysis of immunoglobulin variable domain sequences and T cell receptor (TR) sequences. In addition to performing a regular Blast search, igblast

• Reports the germline V, D and J gene matches to the query sequence. Annotates the immunoglobulin domains (FR1 through CDR3). Reveals the V(D)J junction details such as nucleotide homology between the ends of V(D)J segments and N nucleotide insertions. Indicates the whether the rearrangement is in-frame or out-of-frame.

• igblast docs

• Module Name: igblast (see the modules page for more information)
• Multithreaded
• Reference data in /fdb/igblast/

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load igblast samtools

# Get the chromosome containing mouse Tcra (T-cell receptor alpha chain)
[user@cn3144 ~]$ ln -s /fdb/igenomes/Mus_musculus/NCBI/GRCm38/Sequence/Chromosomes/14.fa

[user@cn3144 ~]$ igblastn \
  -germline_db_V mouse_gl_V \
  -germline_db_J mouse_gl_J \
  -germline_db_D mouse_gl_D \
  -organism mouse \
  -domain_system kabat \
  -query <(samtools faidx 14.fa 14:52427967-54224198) \
  -auxiliary_data optional_file/mouse_gl.aux \
  -show_translation \
  -outfmt 7 

# IGBLASTN 2.6.1+
# Query: 14:52427967-54224198
# Database: mouse_gl_V mouse_gl_D mouse_gl_J
# Domain classification requested: kabat

# V-(D)-J rearrangement summary for query sequence (Top V gene match, Top J gene match, Chain type, stop codon, V-J frame, Productive, Strand).  Multiple equivalent top matches, if present, are separated by a comma.
		    21-11N/AVLYesN/ANo+

# V-(D)-J junction details based on top germline gene matches (V end, V-J junction, J start).  Note that possible overlapping nucleotides at VDJ junction (i.e, nucleotides that could be assigned to either rearranging gene) are indicated in parentheses (i.e., (TACT)) but are not included under the V, D, or J gene itself
		    CAAGGN/AN/A

# Hit table (the first field indicates the chain type of the hit)
# Fields: query id, subject id, % identity, alignment length, mismatches, gap opens, gaps, q. start, q. end, s. start, s. end, evalue, bit score
# 3 hits found
		    V14:52427967-5422419821-1189.15783524121582612159042853671.47e-1690.6
		    V14:52427967-5422419821-1186.905847245232845233642853673.74e-1586.0
		    V14:52427967-5422419821-1186.905847248342948343742853673.74e-1586.0

Total queries = 1
Total identifiable CDR3 = 0
Total unique clonotypes = 0

# BLAST processed 1 queries
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. igblast.sh). For example:

#!/bin/bash
set -e
 
cd /data/$USER/mydir
module load igblast samtools
ln -s /fdb/igenomes/Mus_musculus/NCBI/GRCm38/Sequence/Chromosomes/14.fa
igblastn \
  -germline_db_V mouse_gl_V \
  -germline_db_J mouse_gl_J \
  -germline_db_D mouse_gl_D \
  -organism mouse \
  -domain_system kabat \
  -query <(samtools faidx 14.fa 14:52427967-54224198) \
  -auxiliary_data optional_file/mouse_gl.aux \
  -show_translation \
  -outfmt 7
  -num_threads $SLURM_CPUS_PER_TASK

Submit this job using the Slurm sbatch command, e.g.

sbatch --cpus-per-task=8 --mem=10g igblast.sh

Create a swarmfile (e.g. igblast.swarm). For example:

igblastn   -germline_db_V mouse_gl_V   -germline_db_J mouse_gl_J   -germline_db_D mouse_gl_D \
  -organism mouse   -domain_system kabat   -query <(samtools faidx 14.fa 14:52427967-54224198) \
  -auxiliary_data optional_file/mouse_gl.aux   -show_translation   -outfmt 7
  -num_threads $SLURM_CPUS_PER_TASK
[...]

Submit this job using the swarm command.

swarm -f igblast.swarm [-g #] [-t #] --module igblast