runtime

README.md

 ##### 2. Novoalign
 
 ```bash
-novoalign -d <reference.ndx> -f <read1.fastq.gz> <read2.fastq.gz> -o SAM -c $nt > ${sample}.novoalign.sam
+novoalign -d <reference.ndx> -f <read1.fastq.gz> <read2.fastq.gz> -o SAM -c $nt --hlimit 9 -t 0,2 > ${sample}.novoalign.sam
 ```
 
 ##### 3. covert sam to bam and index bam
 
 ##### Per sample running time
 
-to be added
+| Module    | Time    |
+| --------- | ------- |
+| Novoalign | 13h     |
+| SamToBam  | 3h40min |
+| indexBam  | 15min   |
+| Dedup     | 20min   |
+