BWA Benchmark (ODROID C2,RPI3)

BWA Benchmark

BWA Setup instructions

• Retrieve https://sourceforge.net/projects/bio-bwa/files/bwa-0.6.2.tar.bz2/download
  • Patch the Makefile:
    • Add to DFLAGS: -std=gnu90 -D_NO_SSE2
  • Compile BWA
• Retrieve ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF_000005845.2_ASM584v2/GCF_000005845.2_ASM584v2_genomic.fna.gz
• Retrieve https://s3.amazonaws.com/public.ged.msu.edu/ecoli_ref-5m-trim.fastq.gz
• Run gunzip GCF_000005845.2_ASM584v2_genomic.fna.gz
• Run gunzip ecoli_ref-5m-trim.fastq.gz
• Run bwa index GCF_000005845.2_ASM584v2_genomic.fna

Running Benchmark

Benchmark command

• 1 thread
  • bwa aln GCF_000005845.2_ASM584v2_genomic.fna ecoli_ref-5m-trim.fastq > /dev/null
• 4 threads
  • bwa aln -t4 GCF_000005845.2_ASM584v2_genomic.fna ecoli_ref-5m-trim.fastq > /dev/null