Awesome Bioinformatics Awesome Build Status

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


Data Processing

Command Line Utilities

Next Generation Sequencing

Pipelines/Pipeline frameworks

Sequence Processing

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

Sequence Alignment

De Novo Alignment

DNA Resequencing

Variant Calling

BAM File Utilities

VCF File Utilities

GFF BED File Utilities

Variant Simulation

Variant Filtering / Quality Control

Variant Prediction/Annotation

Python Modules

Data

Tools

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

Sequencing

RNA-Seq

ChIP-Seq

YouTube Channels and Playlists

Blogs

Miscellaneous

License

CC0