Table 1 List of software and tools used for analysis.

From: Benchmarking of variant calling software for whole-exome sequencing using gold standard datasets

Variant calling software

Software version

Tool/application

Version

Pipelines

Computing location

Price model

Cost (SGD)

Illumina

Basespace

Sequence Hub

N.A.

DRAGEN Enrichment

4.2.7

DRAGEN with machine learning

Cloud

Annual subscription  +  credits

$735d

CLC

Genomics

Workbench

23.0.5

LightSpeed Fastq to Germline Variants

23.1

Unknown

Clouda

or

Local PCb

Annual subscription

$22,249e or $8450f

Partek flow

11.0.24.0325

BWA-MEM

0.7.17

Manual configuration

Cloudc

Annual subscription

$7828

GATK

4.2

FreeBayes

1.3.6

Samtools

1.4.1

Varsome clinical

11.14

Single sample germline analysis

Unknown

Sentieon (bwa-mem) aligner & Sentieon DNAscope caller

Cloud

Charged by base count or variant count per sample

$2490g

  1. aUser must already be subscribed to Amazon Web Service to use this software for cloud analysis.
  2. bIntel Xeon Gold 5218 @ 2.30 GHz x 32, 64GB RAM, Linux OS. Analysis was performed on this local PC in this study.
  3. c40 cores, 503.80GB RAM, Linux OS.
  4. dCost is for annual subscription which comes with credits and 1 TB storage, additional credits can be purchased separately; $1,463 for 1,000 credits.
  5. eCost is for CLC Genomics Workbench Desktop Premium version and Cloud Module.
  6. fCost is for CLC Genomics Workbench Desktop Premium version.
  7. gEstimated cost for this project. Cost can be variable due to tiered pricing for different increments of base/variant counts.
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