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**Compile BWA | **Compile BWA | ||
*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 | *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 GCF_000005845.2_ASM584v2_genomic.fna.gz | ||
*Run gunzip ecoli_ref-5m-trim.fastq.gz | *Run gunzip ecoli_ref-5m-trim.fastq.gz | ||
Revision as of 11:42, 30 July 2016
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
- 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
