Bioinformatics Open Source Projects

List of Computer Science courses with video lectures.

Data Apps & Dashboards for Python. No JavaScript Required.

Official git repository for Biopython (originally converted from CVS)

A curated list of awesome Bioinformatics libraries and software.

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

A DSL for data-driven computational pipelines

Single-cell analysis in Python. Scales to >100M cells.

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

A versatile pairwise aligner for genomic and spliced nucleotide sequences

MMseqs2: ultra fast and sensitive search and clustering suite

Useful bash one-liners for bioinformatics.

A curated list of awesome deep learning applications in the field of computational biology

Official code repository for GATK versions 4 and up

A full spaCy pipeline and models for scientific/biomedical documents.

Conda recipes for the bioconda channel.

This library provides implementations of many algorithms and data structures that are useful for bioinformatics. All provided implementations are rigorously tested via continuous integration.

Data intensive science for everyone.

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

resources for learning bioinformatics

A cross-platform and ultrafast toolkit for FASTA/Q file manipulation

Toolkit for processing sequences in FASTA/Q formats

Aggregate results from bioinformatics analyses across many samples into a single report.

Unix, R and python tools for genomics and data science

Foldseek enables fast and sensitive comparisons of large structure sets.

Therapeutics Commons (TDC): Multimodal Foundation for Therapeutic Science

scikit-bio: a community-driven Python library for bioinformatics, providing versatile data structures, algorithms and educational resources.

Pytorch Repo for DeepGCNs (ICCV'2019 Oral, TPAMI'2021), DeeperGCN (arXiv'2020) and GNN1000(ICML'2021): https://www.deepgcns.org

Protein Graph Library

A Deep Learning Toolkit for DTI, Drug Property, PPI, DDI, Protein Function Prediction (Bioinformatics)

A cross-platform, efficient and practical CSV/TSV toolkit in Golang

A python library for multi omics included bulk and single cell RNA-seq analysis.

A cross-platform command-line tool for executing jobs in parallel

Robust, flexible and resource-efficient pipelines using Go and the commandline

Circular visualization in Python (Circos Plot, Chord Diagram, Radar Chart)

A plotly.js React component from Plotly 📈

Scripts to download genomes from the NCBI FTP servers

Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments

Cloud-native genomic dataframes and batch computing

ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.

A comprehensive tutorial about GWAS and PRS

A language and runtime for distributed, incremental data processing in the cloud

A comprehensive library for computational molecular biology

C library for high-throughput sequencing data formats

Empower Large Language Models (LLM) using Knowledge Graph based Retrieval-Augmented Generation (KG-RAG) for knowledge intensive tasks

Python library to facilitate genome assembly, annotation, and comparative genomics

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

A curated list of Cheminformatics libraries and software.

Specification for the Workflow Description Language (WDL).

The next version of bwa-mem

Python package for graph neural networks in chemistry and biology

Plant phenotyping with image analysis

A fast and sensitive gapped read aligner

Python and C++ code for reading and writing genomics data.

Bioinformatics containers

Precision Medicine Knowledge Graph (PrimeKG)

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more

Tools to process and analyze deep sequencing data.

Awesome resources on Bioinformatics, data science, machine learning, programming language (Python, Golang, R, Perl) and miscellaneous stuff.