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=BWA Benchmark=
=BWA Benchmark=
BWA is a tool for mapping reads against a genome. This is nice for doing a non-synthetic benchmark, as meaningful work is done, and IO, Memory and CPU is all used.
==BWA Setup instructions==
==BWA Setup instructions==
*Retrieve https://sourceforge.net/projects/bio-bwa/files/bwa-0.6.2.tar.bz2/download
*Retrieve https://sourceforge.net/projects/bio-bwa/files/bwa-0.6.2.tar.bz2/download

Revision as of 12:51, 30 July 2016

BWA Benchmark

BWA is a tool for mapping reads against a genome. This is nice for doing a non-synthetic benchmark, as meaningful work is done, and IO, Memory and CPU is all used.

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