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

	Tool	Version	Reference
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]