Yoga is an embeddable layout engine targeting web standards.

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

A single molecule sequence assembler for genomes large and small.

Ultra-fast and memory-efficient (meta-)genome assembler

a Bioinformatics Application for Navigating De novo Assembly Graphs Easily

hybrid assembly pipeline for bacterial genomes

Signal-level algorithms for MinION data

Raw nanopore signal mapper that enables real-time targeted sequencing

Fast genome and metagenome distance estimation using MinHash

adapter trimmer for Oxford Nanopore reads

Avogadro 1 is not under active development, the repository was archived in September 2021. Development of Avogadro 2 is being done at https://github.com/openchemistry/avogadrolibs. Avogadro is an a…

quality filtering tool for long reads

Automatically exported from code.google.com/p/sse2neon

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr.214270.116 Note: This was the original repository which wil…

A fast approximate aligner for long DNA sequences

[MOVED] Moved to paoloshasta/shasta. De novo assembly from Oxford Nanopore reads

Classifier for metagenomic sequences

De novo genome assembler for long uncorrected reads

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads

Bifrost: Highly parallel construction and indexing of colored and compacted de Bruijn graphs

A simple and fast metassembler and assembly gap filler designed for long molecule based assemblies.

GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html Note: This was the original repository which…

Pan-genome inference and genotyping with long noisy or short accurate reads

Kmer-db is a fast and memory-efficient tool for large-scale k-mer analyses (indexing, querying, estimating evolutionary relationships, etc.).

Minia is a short-read assembler based on a de Bruijn graph

Graphical interactive tool for the visualization of sequence graphs in GFA format.

✏️ Genome assembly polishing & SNV detection

Split Kmer Analysis

Fast and precise comparison of genomes and metagenomes (in the order of terabytes) on a typical personal laptop

A modification to the slurm_showq code written by TACC.