Quick NGS All-in-one data processing for Next-Generation Sequencing

External tools used by QuickNGS


For the core analysis of the raw data, we have carefully selected the most appropriate previously published algorithmic approaches. The selection criteria were:

  • Performance in published and in-house benchmarking studies
  • Comprehensiveness of the analysis output
  • Quality of the implementation and steadiness of maintenance
  • Popularity in the community
To our perception, our choice of algorithms is the best to meet these criteria as far as possible.

Tools used by the main QuickNGS platform

The following table gives an overview of the tools that are being adopted alongside with the version used in QuickNGS 1.1.0.


ApplicationTool VersionReference
RNA-SeqFastQC0.10.1
Tophat22.0.10Kim et al., Genome Biol, 2013
Cufflinks22.1.1Trapnell et al., Nat Biotechnol, 2010
DESeq21.10.0Anders et al., Genome Biol, 2010
DEXSeq1.16.0Anders et al., Genome Res, 2012
UCSC Genome Browser Kent et al., Genome Res, 2002
miRNA-SeqFastQC0.10.1
miRDeep20.0.5Friedländer et al, Nat Biotechnol, 2008
DESeq21.10.0Anders et al., Genome Biol, 2010
UCSC Genome BrowserKent et al., Genome Res, 2002
ChIP-SeqFastQC0.10.1
BWA0.7.7Li et al., Bioinformatics, 2009
MACS22.0.10Feng et al., Nat Protocols, 2012
MEME-ChIP4.10.0Machanick et al., Bioinformatics, 2011
UCSC Genome Browser Kent et al., Genome Res, 2002
WGSFastQC0.10.1
BWA0.7.7Li and Durbin, Bioinformatics, 2009
Samtools1.2Li et al., Bioinformatics, 2009
Delly2.0.1Rausch et al., Bioinformatics, 2012
SnpEff3.4Cingolani et al., Fly, 2012
UCSC Genome Browser Kent et al., Genome Res, 2002


Tools used by QuickNGS Cancer

From version 1.2.0, QuickNGS contains a suite of pipelines specifically designed for cancer genome analysis. The tools used by this platform entitled QuickNGS Cancer are listed in the table below.


ApplicationTool VersionReference
RNA-Seq CancerFastQC0.10.1
Tophat22.0.10Kim et al., Genome Biol, 2013
JAFFA1.0.7Davidson et al., Genome Med, 2015
Cufflinks22.1.1Trapnell et al., Nat Biotechnol, 2010
DESeq21.10.0Anders et al., Genome Biol, 2010
DEXSeq1.16.0Anders et al., Genome Res, 2012
UCSC Genome Browser Kent et al., Genome Res, 2002
WGS CancerFastQC0.10.1
BWA0.7.7Li and Durbin, Bioinformatics, 2009
GATK3.3.0McKenna et al., Genome Res, 2010
Delly2.0.1Rausch et al., Bioinformatics, 2012
VarScan22.3.7Koboldt et al., Genome Res, 2012
MuTect1.1.4Cibulskis et al., Nat Biotechnol, 2013
SomaticSniper1.0.5.0Larson et al., Bioinformatics, 2012
Strelka1.0.15Saunders et al., Bioinformatics, 2012
SnpEff3.4Cingolani et al., Fly, 2012
EXCAVATOR1.1Magi et al., Genome Biol, 2013
ExomeDepth1.1.6Plagnol et al., Bioinformatics, 2012
TitanCNA1.8.0Ha et al., Genome Res, 2014
UCSC Genome Browser Kent et al., Genome Res, 2002
WXS CancerFastQC0.10.1
BWA0.7.7Li and Durbin, Bioinformatics, 2009
GATK3.3.0McKenna et al., Genome Res, 2010
Delly2.0.1Rausch et al., Bioinformatics, 2012
VarScan22.3.7Koboldt et al., Genome Res, 2012
MuTect1.1.4Cibulskis et al., Nat Biotechnol, 2013
SomaticSniper1.0.5.0Larson et al., Bioinformatics, 2012
Strelka1.0.15Saunders et al., Bioinformatics, 2012
SnpEff3.4Cingolani et al., Fly, 2012
EXCAVATOR1.1Magi et al., Genome Biol, 2013
ExomeDepth1.1.6Plagnol et al., Bioinformatics, 2012
TitanCNA1.8.0Ha et al., Genome Res, 2014
UCSC Genome Browser Kent et al., Genome Res, 2002
Ampl-Seq CancerFastQC0.10.1
BWA0.7.7Li and Durbin, Bioinformatics, 2009
GATK3.3.0McKenna et al., Genome Res, 2010
Delly2.0.1Rausch et al., Bioinformatics, 2012
SnpEff3.4Cingolani et al., Fly, 2012
UCSC Genome Browser Kent et al., Genome Res, 2002

The software for QC and vizualisation as well as for data management and the workflow itself is unique to QuickNGS. As a reference to genomic sequence and annotation, the system uses the miRBase (miRNA-Seq) as well as the Ensembl database (all other applications).


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News

June 6th, 2017: Our paper on the cancer genome analysis platform QuickNGS Cancer has been published in Human Mutation.

September 30th, 2016: Please access the 'Multi-Layer Integration' area to combine RNA-Seq and ChIP-Seq data with an early release of our new multi-OMICS data integration platform.

June 23rd, 2016: Tools for gene set enrichment analysis using GO terms and KEGG pathways have been adopted into QuickNGS from version 1.2.2 on.

February 15th, 2016: The latest QuickNGS release now includes QuickNGS Cancer, a new platform specifically designed for cancer genome analysis.

January 4th, 2016: Bluebee High-Performance Genomics B.V., Delft, The Netherlands, have adopted QuickNGS into their cloud-based NGS analysis solution.

September 23rd, 2015: Please refer to our new FAQ to handle common problems with the QuickNGS results.

July 31th, 2015: The QuickNGS paper was published in BMC Genomics! Please cite this paper for all analyses based on the QuickNGS system.

July 11th, 2014: The first public version of the QuickNGS source code has just been released! Please click here to download the software.