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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 11:51, 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
- 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 with command: make
- Patch the Makefile:
- 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
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 |
