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=BWA Benchmark=
=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 ttps://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


==BWA Setup instructions==
 
==Results==

Revision as of 11:42, 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

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