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Tools and software to be used in the CTLGH Bioinformatics workshop from Feb 13-17.
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bioinformatics-workshop-apps.md

CTLGH BioInformatics Workshop; Tools & Software

R software/IDE

R

RStudio

  • WIP

Python 2.7 and Python Module(s)

Quality Control

FastQC

ea-utils

RSeQC

Alignment

BWA

samtools

STAR

HiSAT2

Quantification

HTSeq

Kallisto

Differential Expression

edgeR, DeSeq2 & Sleuth

  • These are R/3.3.2 packages

    • loadable by first loading R/3.3.2 module & then using library() function to load each package

  • sample usage:

      $ module load R/3.3.2
  $ R
  > library(edgeR)
  > library(DESeq2)
  > library(sleuth)

Functional Analysis

GSEA

GoSeq

  • An R/3.3.2 package

    • loaded by loading R/3.3.2 & then using library() function to load it

  • sample usage:

      $ module load R/3.3.2
  $ R
  > library(goseq)

Variant Calling

Picard

GATK

Variant Filtering/Annotation

VEP

  • Wiki URL: http://hpc.ilri.cgiar.org/vep-software

  • latest version: vep/87

  • sample usage:

      $ module load vep/87
  $ variant_effect_predictor.pl

  • Annotation data(including B. taurus) in: /export/data/bio/vep/

VCFtools

Visualization

IGV

Association

Plink

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