Top 704 bioinformatics open source projects

🐣 locally query the ncbi taxonomy

Javascript full-stack framework for Big Data visualisation and analysis

Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model

memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping

Efficient variant-call data storage and retrieval library using the TileDB storage library.

A wrapper for the EnsEMBL REST API

Fast & accurate alignment of barcoded short-reads

(No maintenance) Detect gene fusion directly from raw fastq files

(formerly eelpond) an automated RNA-Seq workflow system

JAMP - Just Another Metabarcoding Pipeline

highly-efficient & lightweight mutation signature matrix aggregation

an implementation of NSGA-II in java

DEPRECIATED! Please use nf-core/tools instead

Data and analysis for the Splatter paper

A Python package for fast operations on 1-dimensional genomic signal tracks

A robust model for quantitative comparison of ChIP-Seq data sets.

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

Data intensive science for everyone.

Toolkit for processing sequences in FASTA/Q formats

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

Scalable genomic data analysis.

A plotly.js React component from Plotly 📈

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

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

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

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

Unix, R and python tools for genomics and data science

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

List of Computer Science courses with video lectures.

C library for high-throughput sequencing data formats

Scripts to download genomes from the NCBI FTP servers

Biostar Q&A

BWK awk modified for biological data

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

Tools to process and analyze deep sequencing data.

Versatile open-source tool for microbiome analysis

MMseqs2: ultra fast and sensitive search and clustering suite

Workflow Description Language - Specification and Implementations

d3 library to build circular graphs

📖🔬☕️ BioJava is an open-source project dedicated to providing a Java library for processing biological data.

Bioinformatics containers

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

Tools for working with SAM/BAM data

The next version of bwa-mem

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

A modern genome browser built with JavaScript and HTML5.

A fast and sensitive gapped read aligner

Signal-level algorithms for MinION data

Plant image analysis using OpenCV

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

Ultra-fast and memory-efficient (meta-)genome assembler

Cutadapt removes adapter sequences from sequencing reads

A scikit-learn compatible library for graph kernels

Working with molecular structures in pandas DataFrames

Open-source bioinformatics components for Dash

Java utilities for Bioinformatics

Interactive network visualization in Python and Dash, powered by Cytoscape.js

Bioinformatics one liners from Ming Tang

Efficient pythonic random access to fasta subsequences