Resources - Software

Essential bioinformatics software and tools — BLAST, GATK, Bioawk, and more. Curated list with descriptions for genomics and sequence analysis.

Software & Tools


General Bioinformatics Tools

  • BLAST
    Description: Tool for sequence alignment and searching databases for sequence similarities.

  • Bioawk
    Description: An extended version of the Unix awk command, tailored for processing biological data.

  • GATK (Genome Analysis Toolkit)
    Description: A suite of tools for variant discovery and genotyping in high-throughput sequencing data.

  • Fastp
    Description: A quality control tool for high-throughput sequence data.

  • FastQC
    Description: A quality control tool for high-throughput sequence data.



R And Associated Software

  • CRAN
    Description: The primary source for installing R on all operating systems.

  • posit Description: For downloading RStudio Desktop (Free Software)

  • The Bioconductor Project Description: Home for many R Packages used during bioinformatics analysis



Workflow Management Systems

  • Snakemake
    Description: A Python-based workflow management tool for reproducible and scalable data analysis.

  • Nextflow
    Description: A workflow framework enabling scalable and reproducible workflows.

  • Cromwell
    Description: A workflow management system designed for portability and scalability.

  • WDL (Workflow Description Language)
    Description: A portable specification language for defining bioinformatics workflows.



RNA-Seq Analysis Tools

  • DESeq2
    Description: R package for differential gene expression analysis.

  • EdgeR
    Description: R package for differential expression analysis of RNA-seq data.

  • HISAT2
    Description: A fast and sensitive alignment tool for mapping RNA-seq reads.

  • STAR
    Description: An RNA-seq aligner optimized for ultrafast alignment.

  • Salmon
    Description: A lightweight tool for transcript-level quantification from RNA-seq data.

  • RNA-seq Analysis with Limma, Glimma, and edgeR
    Description: A step-by-step guide for performing RNA-seq differential gene expression analysis using edgeR, Limma, and Glimma in R.



Data Visualization Resources

  • From Data to Vis
    Description: Provides detailed guidance on selecting and creating graphs for various types of data. Includes examples and links for implementation in R, Python, D3.js, and React.

  • Cheat Sheets for R
    Description: A collection of cheat sheets covering RStudio, ggplot2, dplyr, tidyr, and more, for quick reference and learning.

  • The R Graph Gallery
    Description: A curated collection of graph examples created using R, along with code snippets and customization tips.

  • Awesome ggplot2
    Description: A GitHub repository with links to packages, books, tutorials, and resources for data visualization using ggplot2.

  • Top R Colour Palettes
    Description: Examples of color palettes for data visualization in R, including RColorBrewer, viridis, and ggplot2 palettes.

  • IGV (Integrative Genomics Viewer)
    Description: A tool for visualizing large-scale genomic datasets.

  • Tableau Public
    Description: A data visualization platform for creating interactive dashboards.

  • Plotly
    Description: A graphing library for Python and R, enabling interactive visualizations.



Metagenomics Tools

  • QIIME2
    Description: A platform for analyzing and visualizing microbiome data.

  • Kraken2
    Description: A taxonomic sequence classification system.

  • MetaPhlAn
    Description: A tool for profiling the composition of microbial communities.



Variant Calling Tools & Genomic Analysis

  • PLINK
    Description: A toolset for genome-wide association studies and population genetics.

  • FreeBayes
    Description: A haplotype-based variant detector.

  • bcftools
    Description: Command-line tools for variant calling and manipulating VCF files.



Structural Variant Analysis

  • LUMPY
    Description: A structural variant detection tool.

  • Manta
    Description: A tool for calling structural variants and indels.



Additional Useful Tools

  • Cytoscape
    Description: A tool for visualization and analysis of networks.

  • JupyterLabs Description: Home for Jupyter Notebooks

  • Docker
    Description: A platform for creating and running containers for reproducible workflows.

  • Singularity
    Description: A container system optimized for HPC environments.

  • Galaxy
    Description: An open-source platform for reproducible bioinformatics research.

  • UCSC Genome Browser
    Description: An interactive tool for exploring genome annotations.



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