Find open-source science resources

Ultra-fast, sensitive search and clustering suite for protein and nucleotide sequence sets.

Freely available tools for biological computing in Python, with included cookbook, packaging and thorough documentation. Part of the [Open Bioinformatics Foundation](http://open-bio.org/). Contains the very useful [Entrez](https://biopython.org/DIST/docs/api/Bio.Entrez-module.html) package for API access to the NCBI databases.

A compressor of common genomic file formats (BAM, CRAM, FASTQ, VCF etc).

samtools/bcftools are a suite of tools for manipulating NGS data and can be used to call variants.

A Workflow Management System geared towards scientific workflows.

A haplotype-resolved assembler for accurate Hifi reads.

A small language for defining pipeline stages and linking them together to make pipelines.

The modern C++ library for sequence analysis.

Structural variant discovery by integrated paired-end and split-read analysis.

Sequence manipulation toolkit for FASTA/FASTQ files written in Nim.

A quality control tool for high throughput sequence data.

Utilities for working with CSV/Tab-delimited files.

Suite of tools to handle gene annotations in any GTF/GFF format.

Cython + HTSlib == fast VCF parsing; even faster parsing than pyVCF.

Pythonic Access to the Ensembl database.

SPAdes (St. Petersburg genome assembler) is an assembly toolkit containing various assembly pipelines and the de-facto standard for prokaryotic genome assemblies.

fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing.

Another cross-platform, efficient, practical and pretty CSV/TSV toolkit.

Access to Biological Web Services from Python.

A list of pipeline resources.

A python-based workflow manager.

GFF and GTF file manipulation and interconversion.

Deep learning-based variant caller

Genetic variant annotation and effect prediction toolbox.

A single molecule sequence assembler for genomes large and small.

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.

a specification for describing analysis workflows and tools that are portable and scalable across a variety of software and hardware environments, from workstations to cluster, cloud, and high performance computing (HPC) environments.

Prokka: rapid prokaryotic genome annotation. Prokka is one of the most cited annotation command line tools for microbial genome annotations.

Biocaml aims to be a high-performance user-friendly library for Bioinformatics.

Sort genomic files according to a specified order.

SIMD C library for global, semi-global, and local pairwise sequence alignments

A circos representation of multiple GWAS results.

GRIDSS: the Genomic Rearrangement IDentification Software Suite.

Collection of tools for working with BAM files.

Burrow-Wheeler Aligner for pairwise alignment between DNA sequences.

A Swiss Army knife for genome arithmetic.

A system for rapidly aligning entire genomes, whether in complete or draft form.

A Go library and command line utility for engineering organisms.

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.

UNIX-style FASTA manipulation tools.

structural variant calling and genotyping with existing tools, but,smoothly.

A collection of research papers for AI-based protein design.

file format conversion in Biopython in a convenient way.

Predicts whether an amino acid substitution affects protein function.