How to use:

Available versions and modules:

VersionModule
2.2.1bioinfo/bwa-mem2

Example:

  • This example can be found on the official git page (bwa-mem2)
  • you need to download human_g1k_v37.fasta
indexing.sge
#!/bin/bash
#$ -N bwa-mem2_indeksiranje
#$ -cwd
#$ -pe p28-mpisingle 2
#$ -l memory=40

module load bioinfo/bwa-mem2/2.2.1  

bwa-mem2 index human_g1k_v37.fasta


In case of large input data

For indexing you need large amount of RAM memory. It is roughly 28 GB of RAM per GB of data. You need to use -l memory parameter to be sure you will have enough memory available. Use p20 and p28 ques as they have 120 GB of RAM memory available. Requested memory with -l memory parameter is per requested core ( in the example above the system will reserve 80 GB of RAM, 2 x 40GB). bwa-mem2 doesn't use more then one core. To get more memory for indexing do not increase core number but increase memory.



bwa-mem2.sge
#!/bin/bash
#$ -N bwa-mem2
#$ -cwd
#$ -pe *mpisingle 16

module load bioinfo/bwa-mem2/2.2.1

bwa-mem2 mem -t $NSLOTS human_g1k_v37.fasta human_g1k_v37.fasta SRR7733443_1.fastq SRR7733443_2.fastq > d3_align.sam
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