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BLAST+

BLAST+ consists of a number of command-line applications for sequence database search, filtering and comparing tools, creating blast databases and masking low complexity sequence.

BLAST+ is available as a module on Apocrita.

Usage

To run the latest installed version of BLAST+, simply load the blast+ module:

$ module load blast+
$ blastn -h
USAGE
  blastn [-h] [-help] [-import_search_strategy filename]
    [-export_search_strategy filename] [-task task_name] [-db database_name]
...

Core usage and core limitation in a multithreaded run

  • To ensure that BLAST+ uses the correct number of cores, the -num_threads=${NSLOTS} option should be used.
  • BLAST+ supports a maximum of 32 cores.

A list of all BLAST+ applications and options can be found here.

Example Jobs

Serial job

Here is an example job for BLAST+ using 32 cores.

#!/bin/bash
#$ -cwd
#$ -l h_rt=5:0:0
#$ -l h_vmem=7.5G
#$ -pe smp 32

module load blast+

blastn -num_threads ${NSLOTS} \
       -out blast_serial.tsv \
       -outfmt 6 \
       -db nt \
       -query GRCh38_chr1_1percent.fasta

References