Find open-source science resources
A directory of tools, AI models, datasets, and research resources for biotech, bioinformatics, and other scientific fields. Aggregated from curated GitHub awesome-lists, HuggingFace, bio.tools, Bioconductor, and more.
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44 of 6,573 resources
A flexible pipeline, built with Nextflow, for the complete analysis of bacterial genomes.
Java-based browser. Fast, efficient, scalable visualization tool for genomics data and annotations. Handles a large variety of formats.
Rust implementations of algorithms and data structures useful for bioinformatics.
Ultra-fast, sensitive search and clustering suite for protein and nucleotide sequence sets.
Tools for adding mutations to existing `.bam` files, used for testing mutation callers.
Another cross-platform, efficient, practical and pretty CSV/TSV toolkit.
Fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs.
Python wrapper for [samtools](https://github.com/samtools/samtools).
BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.
A cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang.
Utilities for working with CSV/Tab-delimited files.
Cython + HTSlib == fast VCF parsing; even faster parsing than pyVCF.
Annotate a VCF with other VCFs/BEDs/tabixed files.
A Swiss Army knife for genome arithmetic.
A Go library and command line utility for engineering organisms.
A haplotype-resolved assembler for accurate Hifi reads.
Modular and universal bioinformatics, Bionode provides pipeable UNIX command line tools and JavaScript APIs for bioinformatics analysis workflows.
fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing.
Bayesian haplotype-based polymorphism discovery and genotyping.
Fast FASTQ filtering by matching reads against one or more regex patterns.
GFF and GTF file manipulation and interconversion.
A C++ library for parsing and manipulating VCF files.
FASTQ and SAM quality control using Python.
BWA-MEM drop-in replacement: 2-3x faster, 2-5x cheaper, 100% identical output on standard CPUs.
lumpy: a general probabilistic framework for structural variant discovery.
A polymorphic bayesian genotyping model with wide applicability.
Sort genomic files according to a specified order.
Toolkit for processing sequences in FASTA/Q formats.
Collection of tools for working with BAM files.
Batteries included genomic analysis pipeline for variant and RNA-Seq analysis, structural variant calling, annotation, and prediction.
Workflow library embedded in the Go programming language, focusing on supporting complex workflow constructs, compiling to a single binary, providing powerful file naming and comprehensive audit reports for every output
Resources on ChIP-seq data which include papers, methods, links to software, and analysis.
Predicts whether an amino acid substitution affects protein function.
Easily submitting PBS jobs with script template. Multiple input files supported.
Go Get Data; A command line interface for obtaining genomic data.
[@crazyhottommy](https://github.com/crazyhottommy)'s notes on various steps and considerations when doing RNA-seq analysis.
Computation Pipeline library for python widely used in science and bioinformatics.
Easy-to-use DNA sequence visualization tool that turns FASTA files into browser-based visualizations.
Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data.