Find open-source science resources

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

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

A flexible pipeline, built with Nextflow, for the complete analysis of bacterial genomes.

An ultrafast protein aligner for `blastp` and `blastx` like searches.

Scalable toolkit for analyzing single-cell gene expression data, including preprocessing, visualization, clustering, and trajectory inference.

Scalable genomic analysis.

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

Python library for blazing-fast genomic interval operations and genomic file formats I/O on Polars DataFrames

Java framework for processing biological data.

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.

A software package for estimating gene and isoform expression levels from RNA-Seq data.

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

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.

Fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs.

A quality control tool for high throughput sequence data.

Python wrapper for [samtools](https://github.com/samtools/samtools).

A python-based workflow manager.

JavaScript genome browser that is highly customizable via plugins and track customizations.

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

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

the wavefront alignment algorithm (WFA) which expoit sequence similarity to speed up alignment

A Workflow Management System geared towards scientific workflows.

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.

The modern C++ library for sequence analysis.

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

Pythonic Access to the Ensembl database.

A list of pipeline resources.

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

Utilities for working with CSV/Tab-delimited files.

International association of users & developers of open source Perl tools for bioinformatics, genomics and life sciences.

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

Burrow-Wheeler Aligner for pairwise alignment between DNA sequences.

A single molecule sequence assembler for genomes large and small.

Annotate a VCF with other VCFs/BEDs/tabixed files.

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

Access to Biological Web Services from Python.

A Swiss Army knife for genome arithmetic.

A Go library and command line utility for engineering organisms.

An ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.

A haplotype-resolved assembler for accurate Hifi reads.

Minimap2 is an pairwise aligner for genomic and spliced nucleotide sequences. It can perform the assembly-to-assembly alignment, and works with gzip'd FASTQ, FASTA formats. It also finds overlaps between long-reads.

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

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.

De novo assembler for single molecule sequencing reads using repeat graphs.