Running and Verifying BWA

Procedure

Use PuTTY to log in to the server as the root user.
Create a working directory for BWA.
```
mkdir -p /path/to/CASE
```
Go to the test file directory.
```
cd /path/to/CASE
```

Obtain the test cases.

wget https://ftp.sra.ebi.ac.uk/vol1/fastq/ERR104/008/ERR1044518/ERR1044518_1.fastq.gz
wget https://ftp.sra.ebi.ac.uk/vol1/fastq/ERR104/008/ERR1044518/ERR1044518_2.fastq.gz
wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_full_analysis_set.fna.gz -O hs38DH.fasta

Decompress the test files.

gzip -d ERR1044518_1.fastq.gz
gzip -d ERR1044518_2.fastq.gz

Create an index file.
```
bwa index -a bwtsw hs38DH.fasta
```
Run the test.
```
bwa mem -t 128 hs38DH.fasta ERR1044518_1.fastq ERR1044518_2.fastq > bwa.sam 2 > bwa_log
```
The number 128 indicates the number of used cores. You can change the number according to the server configuration.

Check the value of Real time (unit: s) in the bwa_log log. A smaller value indicates higher performance.

Parent topic: BWA 0.7.17 Porting Guide (CentOS 7.6)