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 |