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


Results

Device ARCH Kernel OS GCC 1 thread walltime (sec.) 4 thread walltime (sec.)
PC (?@?GHz) x86_64 102.149 34.774
PC (i7-6700k@4.5 GHz) x86 4.6.4-301.fc24.x86_64 Fedora 24 6.1.1 144.221 53.833
PC (i7-6700k@4.5 GHz) x64 4.6.4-301.fc24.x86_64 Fedora 24 6.1.1 77.836 27.840
PC (i7-980x@4.0 GHz) x64 4.6.4-301.fc24.x86_64 Fedora 24 6.1.1 130.605 45.549
ODROID U2 arm7l 3.8.13.30 Ubuntu 14.04.4 LTS 4.8.4 939.300 266.262
ODROID C2 aarch64 3.14.65-73 Ubuntu 16.04 LTS 5.4.0 797.158 235.510
Raspberry Pi 3 aarch64 4.6.4-1-main Fedora 24 6.1.1 1521.175 486.585
Raspberry Pi 3 armv7l 4.6.4-1-main Fedora 24 6.1.1 2172.660 649.805
Raspberry Pi 3 armv7l 4.4.13-v7+ Raspbian Jessie 4.9.2 1224.290 355.897
Orange PI one armv7l 3.4.112 Armbian Jessie 4.9.2 1677.26 486.256
Raspberry Pi zero armv6l 4.4.13+ Raspbian Jessie 4.9.2 2801.69 2812.427
Raspberry Pi 1 armv6l 4.4.13+ Raspbian Jessie 4.9.2 4031.349 4072.279
Raspberry Pi 2 armv7l 4.4.13-v7+ Raspbian Jessie 4.9.2 2009.622 592.694