Useful bioinformatics software packages in Linux

Go back to parent page Introduction to Linux for bioinformatics

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Below I have compiled a non-exhaustive list of useful bioinformatics software packages. First check with your software center whether the packages are available. If not, follow the installation instructions on the the webpage of the package.

UGene, an integrated bioinformatics suite

See http://ugene.net/

UGene is available via the Software Manager in Ubuntu-based distributions.

R, the statistical language project

See http://www.r-project.org/

R is the most widely used language for computing and statistical analysis. It can be extended via the CRAN repository. It has also a lot of bioinformatics extensions distributed via http://bioconductor.org/. Every bioinformatician should know at least the basics of R.

Be aware! Installing R on your own machine can take a while. Always use the latest version of R, and update frequently. It will break your scripts from time to time, but there is no reason to postpone upgrading, since the new R code is better, faster and stronger then before.

Be aware! Some extensions are not maintained well, and become obsolete while R advances to next versions.

RStudio

See https://www.rstudio.com/

A very popular and powerful graphical interface to R. It comes with productivity enhancing extensions, such as RMarkdown and knitr extensions to document your code easily, help search screen, and more.

IGV, the integrative genomics viewer

See http://www.broadinstitute.org/igv/

The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large genomic datasets.

Qualimap suite to analyse quality metrics of NGS data

See http://qualimap.bioinfo.cipf.es/

Qualimap is a platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data.

Cytoscape, a interactive network analysis tool

See http://www.cytoscape.org/

Open-source platform for netwerk analysis and visualisation.

GNU Octave, the open-source matlab clone

See http://www.gnu.org/software/octave/

A powerful numerical computations language, with extensive graphical capabilities.

Multi Experiment viewer, MeV

See http://www.tm4.org/mev.html

MeV is a versatile microarray data analysis tool, incorporating sophisticated algorithms for clustering, visualization, classification, statistical analysis and biological theme discovery.

RapidMiner, data analysis toolkit

See http://rapid-i.com/content/view/181/

Open-source system for data mining. It is available as a stand-alone application for data analysis and as a data mining engine for the integration into own applications.

bedtools

See https://github.com/arq5x/bedtools2

BEDTools utilities address common genomics tasks such as finding feature overlaps and computing coverage.

SAMtools

See http://www.htslib.org/

SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.

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Go back to parent page Introduction to Linux for bioinformatics