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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

From: QuickNGS elevates Next-Generation Sequencing data analysis to a new level of automation

  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]