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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