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**Patch the Makefile:
**Patch the Makefile:
***Add to DFLAGS: -std=gnu90 -D_NO_SSE2
***Add to DFLAGS: -std=gnu90 -D_NO_SSE2
**Compile BWA
**Compile BWA with command: make
 
*Retrieve ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF_000005845.2_ASM584v2/GCF_000005845.2_ASM584v2_genomic.fna.gz
*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
*Retrieve https://s3.amazonaws.com/public.ged.msu.edu/ecoli_ref-5m-trim.fastq.gz

Revision as of 12:49, 30 July 2016

BWA Benchmark

BWA Setup instructions

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


Results

Device ARCH OS Kernel GCC 1 thread walltime 4 thread walltime
ODROID U2 armhf 3.8.13.30 Ubuntu 14.04.4 LTS 4.8.4
ODROID C2 aarch64 Ubuntu 16.04 LTS
Raspberry PI 3 aarch64 Fedora 24