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BWA

BWA is alignment software developed for mapping short sequences from next-generation sequencing to reference sequences (in FASTA format). The reference sequence must be indexed first. Depending on the sequencing method, it supports single-end (SE) and paired-end (PE) alignment.

1. Script Template​

submit.sh
#!/bin/bash
#SBATCH --nodes=1                   # Number of nodes
#SBATCH --ntasks-per-node=56        # Number of cores per node
#SBATCH --ntasks=56                 # Total number of cores
#SBATCH --partition=g1_share        # Queue partition; must specify the correct partition
#SBATCH --job-name=hello            # Job name
#SBATCH --output=hello.%j.out       # Normal log output (%j parameter value is jobId)
#SBATCH --error=hello.%j.err        # Error log output (%j parameter value is jobId)
   
##############################################
#          Software Envrironment             #
##############################################
unset I_MPI_PMI_LIBRARY                        # Unset default MPI library, use Intel's built-in
export I_MPI_JOB_RESPECT_PROCESS_PLACEMENT=0   # Parameter modification required for Intel multi-node jobs
module load intel/2022 intelmpi/2022           # Load Intel environment
   
##############################################
#               Run job                      #
##############################################
export OMP_NUM_THREADS=1
   
bwa index ref.fa