929 Open Source Bioinformatics Software Projects
Free and open source bioinformatics code projects including engines, APIs, generators, and tools.
Deepvariant 2087 ⭐
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
Awesome Single Cell 1498 ⭐
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
Fastp 850 ⭐
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
Multiqc 655 ⭐
Aggregate results from bioinformatics analyses across many samples into a single report.
Cromwell 605 ⭐
Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
Getting Started With Genomics Tools And Resources 495 ⭐
Unix, R and python tools for genomics and data science
Biojava 410 ⭐
:book::microscope::coffee: BioJava is an open-source project dedicated to providing a Java library for processing biological data.
Combine Lab Salmon 406 ⭐
🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
Edlib 267 ⭐
Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.
Homebrew Bio 221 ⭐
:beer::microscope: Bioinformatics formulae for the Homebrew package manager (macOS and Linux)
Single Cell Pseudotime 216 ⭐
An overview of algorithms for estimating pseudotime in single-cell RNA-seq data
Dnafeaturesviewer 213 ⭐
:eye: Python library to plot DNA sequence features (e.g. from Genbank files)
Awesome Cancer Variant Databases 192 ⭐
A community-maintained repository of cancer clinical knowledge bases and databases focused on cancer variants.
Goleft 164 ⭐
goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary