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Table 1 Comparison of different systems for variant analysis

From: MC-GenomeKey: a multicloud system for the detection and annotation of genomic variants

  STORMseq Atlas2 Simplex WEP GenomeKey MC-GenomeKey
Quality - - fastx-toolkit ngs-qc toolkit + fastqc fastx-toolkit fastx-toolkit
Mapping BWA - BWA BWA BWA BWA
Variant Calling GATK Logistic Regression Model GATK GATK GATK GATK
Annotation VEP (variant effect predictor) - Annovar Annovar Annovar Annovar
Deployment AWS EC2 AWS EC2 AWS EC2 Web Service AWS EC2 AWS, Google Cloud, Amazon, OpenStack based
Web Interface Yes Yes No Yes Yes Yes
Multiple samples in one run No No No No Yes Yes
Parallelization technique split by chromosome - - NA split by chromosome + split by read group id split by chromosome + split by read group id + more split by sub-group ID and sub-chromosomes
Workflow Engine Python Scripts - JClusterService Scripts Cosmos Cosmos
Modularity No - No No Yes Yes
Use of Heterogeneousa cluster No No No NA No Yes
Failure-handling+ Mechanisms No No No No No Yes
Use of Spot Instances No No No NA No Yes
  1. aHeterogeneous cluster means nodes of different virtual machine types and also from different clouds
  2. +Failure handling means response to failure of compute nodes in cloud, as in the case of spot instances