Bioinformatics Tools

Programs marked with W can be used with a web browser and programs marked with C can be used with the Chipster graphical user interface. Programs marked with F are available in the FGI grid environment.

Next generation sequencing data analysis

  • ABySS Assembler for very short reads.
  • ALLPATHS-LG Assembler for very short reads.
  • BEDTools Toolkit for for comparing genomic features. C
  • Bowtie Short read aligner. C
  • Bowtie2 Short read aligner. C, F
  • BWA Burrows-Wheeler aligner for aligning short nucleotide sequences against a reference genome C, F
  • Chipster provides a graphical user interface to over 160 tools for NGS data analysis. It also offers interactive visualizations like genome browser. C
  • Cufflinks RNA-seq analysis tool C
  • FastQC A quality control tool for high throughput sequence data. C
  • GSNAP short read aligner F
  • ipyrad RAD sequence analysis
  • MACS ChIP-Seq analysis tool C
  • MIRA Whole genome shotgun and EST sequence Assembler
  • MISO tool to estimate expression levels of alternatively spliced genes.
  • PANNZER/SANSPANZ Protein annotation tool
  • Prinseq A quality control tool for high throughput sequence data. C
  • R / Bioconductor A statistical environment with support for genomics C
  • SAMtools Utilities for managing SAM/BAM formatted alignment files C, F
  • SHRiMP short read aligner F
  • SOAPdenovo Assembler for very short reads
  • STAR short read aligner
  • TopHat Splice junction mapper for RNA-Seq reads C, F
  • Trimmomatic Tool for trimming illumina data.C
  • Trinity Traskriptome assembly
  • Velvet Assembler for very short reads
  • VirusDetect A tool to indetidy viruses uisng sRNA datasets C

 

Sequence analysis

  • EMBOSS Programs for analysing DNA and amino acid sequence data. CF
  • CD-HIT Sequence clustering and redundancy removal
  • ClustalW Multiple sequence alignment C
  • MAFFT Multiple sequence alignment  C
  • Muscle A fast and accurate multiple sequence alignment

 

Database searching and sequence alignment

  • BLAST Sequence database homology search tool. C, F
  • BLAT Sequence database homology search tool.
  • Exonerate  Generic sequence alignment tool F
  • HMMER Sequence database search based on profile-HMM. C, F
  • InterProScan Protein signature search tool
 

Metagenomics, Phylogenetics and Population Genomics

  • Metagenomics toolkit Selection of metagenomis analysis tools
  • Mothur package for microbial community analysis of amplicon sequencing data C
  • Qiime package for microbial community analysis of amplicon sequencing data
  • BEAST Program for Bayesian MCMC analysis of molecular sequences
  • ExaML Maximum likelihood code phylogenetic inference
  • MrBayes Program for inferring phylogenies using Bayesian methods F
  • PHYLIP Package for inferring phylogenies C
  • POY Program for inferring phylogenies
  • RAxML Fast program for inferring phylogenies with likelihood
  • Stacks pipeline for building loci from short-read sequences (e.g. RAD-seq data)

 

Microarray data analysis

  • Chipster provides a graphical user interface to over 150 tools for microarray data analysis based on R/Bioconductor, and results can be viewed using several interactive visualizations. C
  • R / Bioconductor A statistical environment with support for genomics C

 

Structural Biology

  • Discovery Studio Molecular modeling package D
  • Maestro Molecular modeling package
  • Rosetta Protein structure prediction and protein docking tool
  • VMD Molecular graphics visualisation

 

RNA secondary structure prediction

  • Vienna Package (within EMBOSS) 

 

Gene mapping

  • Mega2 Converts Linkage-format files to other formats
  • MERLIN A fast program for non-parametric linkage, and haplotyping
  • PedCheck Detects marker typing incompatibilities in pedigree data
  • Pseudomarker Joint linkage and LD analysis
  • SimWalk2 Haplotyping, and non-parametric analysis

 

Other tools

  • Bioperl Bioinformatics tools for perl programming
  • Biopython Bioinformatics tools for python programming
  • cPouta Cloud for ruinning own servers and software installations

 

Archived training material

These guides are provided for archival purposes. They may contain outdated instructions and references to software and databases that are no longer available at CSC.

For up-to-date information please refer to the software list and the web pages of each software package.