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Table 2 Performance comparison of Maha-Fs and SGI-UV300

From: Integrated genome sizing (IGS) approach for the parallelization of whole genome analysis

Method

Process Steps

Maha-Fs

SGI-UV300

Core:Memory

4:12

16:64

4:12

16:64

mapping

1. split

35.1

37.7

7.1

7.1

2. sickle

1.2

0.4

2.2

0.2

3. BWA-MEM

9.4

2.5

7.6

3.1

4. Picard-Fix Mate Information

2.6

1.9

4.3

2.7

recalibration

5. Picard-Mark Duplicates

1.5

1.1

7.3

2.7

6. GATK-RealignerTarget Creator

2.9

1.8

4.2

2.7

7. GATK-Indel Re-aligner

1.6

1.1

2.7

1.7

8. GATK-Base Re-calibrator

2.1

1.0

5.5

1.1

9. GATK-Print Reads

2.9

2.2

7.4

3.2

10. GATK-Haplotype Caller

8.0

5.6

10.8

8.1

Time

Total process time (min)

79.8

55.2

59.0

32.5