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Bioinformatics is an interdisciplinary field that develops methods and software tools for understanding biological data. — Wikipedia

A curated list of awesome Bioinformatics software, resources, and libraries. Mostly command line based, and free or open-source. Please feel free to contribute!

Table of Contents


Package suites

Package suites gather software packages and installation tools for specific languages or platforms. We have some for bioinformatics software.

Data Tools

Downloading

Compressing

Data Processing

Command Line Utilities

Next Generation Sequencing

Workflow Managers

Pipelines

Sequence Processing

Sequence Processing includes tasks such as demultiplexing raw read data, and trimming low quality bases.

Data Analysis

The following items allow for scalable genomic analysis by introducing specialized databases.

Sequence Alignment

Pairwise

Multiple Sequence Alignment

Clustering

Quantification

Variant Calling

BAM File Utilities

VCF File Utilities

GFF BED File Utilities

Variant Simulation

Variant Prediction/Annotation

Python Modules

Data

Tools

Assembly

Annotation

Long-read sequencing

Long-read Assembly

Visualization

Genome Browsers / Gene Diagrams

The following tools can be used to visualize genomic data or for constructing customized visualizations of genomic data including sequence data from DNA-Seq, RNA-Seq, and ChIP-Seq, variants, and more.

Database Access

Resources

Becoming a Bioinformatician

Bioinformatics on GitHub

Sequencing

RNA-Seq

ChIP-Seq

YouTube Channels and Playlists

Blogs

Miscellaneous

Online networking groups

License

CC0