Table 1 Algorithms and software tools used by QuickNGS, version 1.1.0 . The selection may be modified, updated or extended in future releases of QuickNGS, however, an up-to-date version of this table will be kept available online at the QuickNGS website

RNA-Seq

FastQC

0.10.1

Tophat2

2.0.10

[12]

Cufflinks2

2.1.1

[19]

DESeq2

1.4.5

[1]

DEXSeq

1.10.5

[2]

UCSC Genome Browser

[11]

miRNA-Seq

FastQC

0.10.1

miRDeep2

0.0.5

[6]

DESeq2

1.4.5

[1]

UCSC Genome Browser

[11]

ChIP-Seq

FastQC

0.10.1

BWA

0.7.7

[13]

MACS2

2.0.10

[5]

MEME-ChIP

4.10.0

[15]

UCSC Genome Browser

[11]

WGS

FastQC

0.10.1

BWA

0.7.7

[13]

Samtools

0.1.19

[13]

Delly

2.0.1

[16]

SnpEff

3.4

[3]

UCSC Genome Browser

[11]