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

A quality control tool for high throughput sequence data.

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.

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

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

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

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

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

Scalable genomic analysis.

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.

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

Java framework for processing biological data.

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

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

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

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

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.

Pythonic access to FASTA files.

Bayesian haplotype-based polymorphism discovery and genotyping.

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.

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

Python wrapper for [bedtools](https://github.com/arq5x/bedtools).

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

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

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.

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

Burrow-Wheeler Aligner for pairwise alignment between DNA sequences.

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

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

Tools for adding mutations to existing `.bam` files, used for testing mutation callers.

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

A Workflow Management System geared towards scientific workflows.

A list of pipeline resources.

Utilities for working with CSV/Tab-delimited files.

A Go library and command line utility for engineering organisms.

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

A python-based workflow manager.

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

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.

A single molecule sequence assembler for genomes large and small.

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

Access to Biological Web Services from Python.

A Swiss Army knife for genome arithmetic.

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.