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The Basic Local Alignment Search Tool (BLAST) is one of the most widely used bioinformatics tools. GPU-BLAST can align query sequences against those present in a selected target database.

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Contents

Glossary

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Overview

Using a general-purpose graphics processing unit (GPU), we have developed GPU-BLAST, an accelerated version of the popular NCBI-BLAST. In comparison to the sequential NCBI-BLAST, GPU-BLAST is nearly four times faster, while producing identical results.

Module: Example

[]$ module spider gpu-blast
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  gpu-blast:
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     Versions:
        gpu-blast/1.1

[]$ module load gpu-blast/1.1

UsingUsing

Use the module name gpu-blast to discover versions available and to load the application.

Basic Command Line

blastp -help

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WARNING: There is no available device supporting CUDA. Continuing with the CPU only...

Example Batch

#!/bin/bash
#SBATCH -J blastp
#SBATCH -t 00:10:00
#SBATCH --mail-type=ALL
#SBATCH --mail-user=<insert-your-email-address>
#SBATCH --account=<insert-your-project-name>
#SBATCH --gres=gpu:1
#SBTACH --partition=moran-gpu

echo "Start:"

module load gpu-blast/1.1
echo "Loaded gpu-blast:"

srun blastp -query queries/SequenceLength_00000100.txt -db database/sorted_env_nr -gpu t -method 1 -gpu_blocks 128 -gpu_threads 32
echo "Finished Successfully:"

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