runtime

README.md

 novoalign -d <reference.ndx> -f <read1.fastq.gz> <read2.fastq.gz> -o SAM -c $nt --hlimit 9 -t 0,2 > ${sample}.novoalign.sam
 ```
 
+![](./pictures/Screen Shot 2019-06-27 at 10.23.47 AM.png)
+
+![](./pictures/Screen Shot 2019-06-27 at 10.22.47 AM.png)
+
 ##### 3. covert sam to bam and index bam
 
 ```bash
 
 ##### Per sample running time
 
+Total ~18h
+
+Settings:
+
+- Disksize 500
+- Cluster OnDemand ecs.sn1ne.8xlarge img-ubuntu-vpc
+- 30x WGS
+
 | Module    | Time    |
 | --------- | ------- |
 | Novoalign | 13h     |