Next Generation Sequencing

There are several pipelines available for analyzing next generation sequencing data. These include:

  • OnTarget
  • TargetCoverage
  • PeakDetector
  • NextGene
  • FilterReads
  • FastRNAMapper
  • SplicingCompass
  • srnaMapper
  • ncRNAAnnotator
  • CompaRNA
  • ChiPeAn

See Analysis Pipelines for detailed descriptions and examples.

 Various other NGS analysis packages are installed on Husar. Please contact us for instructions on how to use them.

  • bfast
  • bowtie
  • bsmap
  • bwa
  • maq
  • novoalign
  • picard
  • rmap
  • sam-tools
  • SNVMix2
  • VarScan
  • GenomeAnalysisTK
  • Velvet
  • MACS
  • QuEST
  • SISSRS
  • spp
  • BEDTools
  • bamtools
  • Useq
  • GATK
  • Annovar
  • FastX-Toolkit
  • Wig-Tools
  • Pearson
  • prinseq
  • homer
  • tophat
last update:
03/03/2014
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