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Step by step instructions to benchmark baseline (bwa-mem) and OpenOmics BWA-MEM (bwa-mem2) on c5.24xlarge and m6i.16xlarge instances of AWS

Step 1: Download datasets

Download reference genome: Homo_sapiens_assembly38.fasta

wget https://storage.googleapis.com/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta

Download dataset #1: ERR194147 (Paired-End) from s3://sra-pub-run-odp/sra/ERR194147/ERR194147

Download dataset #2: ERR1955529 (Paired-End) from s3://sra-pub-run-odp/sra/ERR1955529/ERR1955529

Download dataset #3: ERR3239276 (Paired-End) from s3://sra-pub-run-odp/sra/ERR3239276/ERR3239276

Step 2: Download and compile baseline (BWA v0.7.17) and create index

curl -L https://github.com/lh3/bwa/releases/download/v0.7.17/bwa-0.7.17.tar.bz2 | tar jxf -
cd bwa-0.7.17 && make
./bwa index hs_asm38/Homo_sapiens_assembly38.fasta
cd ..

Step 3: Download OpenOmics BWA-MEM (BWA-MEM2 v2.2.1) and create index

curl -L https://github.com/bwa-mem2/bwa-mem2/releases/download/v2.2.1/bwa-mem2-2.2.1_x64-linux.tar.bz2 | tar jxf -
cd bwa-mem2-2.2.1_x86-linux && ./bwa-mem2 index hs_asm38/Homo_sapiens_assembly38.fasta
cd ..

Step 4: Running baseline and OpenOmics BWA-MEM

The c5.24xlarge instance has 48 cores. The memory available on the instance only allows for using 1 thread per core. On the other hand, the m6i.16xlarge instance has 32 cores. The memory available on the instance allows for using both the threads on each core.

Run baseline BWA-MEM

cd bwa-0.7.17

Sample commands shown below:
For c5.24xlarge:

./bwa mem -t 48 hs_asm38/Homo_sapiens_assembly38.fasta ERR194147_1.fastq ERR194147_2.fastq > ERR194147.out.sam

For m6i.16xlarge:

./bwa mem -t 64 hs_asm38/Homo_sapiens_assembly38.fasta ERR194147_1.fastq ERR194147_2.fastq > ERR194147.out.sam

Run OpenOmics BWA-MEM

cd ../bwa-mem2-2.2.1_x86-linux

Sample commands shown below:
For c5.24xlarge:

./bwa-mem2 mem -t 48 hs_asm38/Homo_sapiens_assembly38.fasta ERR194147_1.fastq ERR194147_2.fastq > ERR194147.out.sam

For m6i.16xlarge:

./bwa-mem2 mem -t 64 hs_asm38/Homo_sapiens_assembly38.fasta ERR194147_1.fastq ERR194147_2.fastq > ERR194147.out.sam