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IgBlast

IgBlast is a sequence analysis tool for immunoglobulin variable domains.

References:

There may be multiple versions of IgBlast available. An easy way of selecting the version is to use modules. To see the modules available, type

module avail igblast

To select a module, type

module load igblast/[ver]

where [ver] is the version of choice.

Environment variables set:

On Helix

Sample session:

module load samtools igblast
# Get the sequence for Tcra (T-cell receptor alpha chain); coordinates taken from NCBI
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 3 \
 -out result.out
The path passed to -auxiliary_data is relative to the directory specified by $IGDATA. The germline databases are found via the BLASTDB environment variable.
Interactive job on Biowulf
sinteractive
module load igblast
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 seq.fasta \
 -auxiliary_data optional_file/mouse_gl.aux \
 -show_translation \
 -outfmt 3 \
 -out result.out
Batch job on Biowulf

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

#!/bin/bash
module load igblast

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 seq.fasta \
 -auxiliary_data optional_file/mouse_gl.aux \
 -show_translation \
 -outfmt 3 \
 -out result.out

Submit this job using the Slurm sbatch command.

sbatch igblast.sh
Swarm of Jobs on Biowulf

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 -auxiliary_data optional_file/mouse_gl.aux -query /data/$USER/myseqs/seq1.fasta -show_translation -outfmt 3 -out /data/$USER/igblastout/seq4.out
igblastn -germline_db_V mouse_gl_V -germline_db_J mouse_gl_J -germline_db_D mouse_gl_D -organism mouse -auxiliary_data optional_file/mouse_gl.aux -query /data/$USER/myseqs/seq2.fasta -show_translation -outfmt 3 -out /data/$USER/igblastout/seq4.out
igblastn -germline_db_V mouse_gl_V -germline_db_J mouse_gl_J -germline_db_D mouse_gl_D -organism mouse -auxiliary_data optional_file/mouse_gl.aux -query /data/$USER/myseqs/seq3.fasta -show_translation -outfmt 3 -out /data/$USER/igblastout/seq4.out
igblastn -germline_db_V mouse_gl_V -germline_db_J mouse_gl_J -germline_db_D mouse_gl_D -organism mouse -auxiliary_data optional_file/mouse_gl.aux -query /data/$USER/myseqs/seq4.fasta -show_translation -outfmt 3 -out /data/$USER/igblastout/seq4.out

Submit this job using the swarm command.

swarm --module igblast -f igblast.swarm 
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