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Table 1 Comparison with previous benchmarks of time and cost for WGS data analysis based on different pipeline and hardware

From: GT-WGS: an efficient and economic tool for large-scale WGS analyses based on the AWS cloud service

Tool Aligner + Variant Caller Depth Time Cost Deptha Timea Costa Hardware
Genomekey + COSMOS [8] BWA + GATK HaplotypeCaller 37× 4.9 h $48.5 55× 7.3 h $72.1 20× AWS c2.8xlarge
Churchill [8] BWA + GATK UnifiedGenotyper 30× 1.7 h 55× 3.1 h 16× AWS r3.8×large
STORMseq [8] BWA + GATK lite 38× 176 h $32.8 55× 255 h $47.5
Crossbow [9] Bowtie + SOAPsnp 38× 4.5 h $71.4 55× 6.5 h $103.3 20× AWS c1.xlarge
Crossbow [9] Bowtie + SOAPsnp 38× 2.5 h $83.6 55× 3.6 h $121 40× AWS c1.xlarge
PEMapper / PECaller [10] PEMapper + PECaller 30× 29.3 h 55× 53.7 h
Globus [11] Bowtie2 + GATK 30× 12 h 55× 22 h 1× AWS cr1.8xlarge
SevenBridges [12] BWA + GATK 15× 8 h $14.1 55× 29.3 h $51.7
BGI-online (BALSA) [13] BALSA 50× 5.5 h 55× 6 h 6-core CPU, 64GB RAM, GPU GTX680
Average       42.9 h $79.1  
  1. a’ means time and cost of different depth data are normalized to 55× with linear relationship. ‘-’ means not reported