SPAdes Genome Assembler

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

Signal-level algorithms for MinION data

Tools for fast and flexible genome assembly scaffolding and improvement

Fast and accurate de novo assembler for long reads

Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets

LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package.

Viral genomics analysis pipelines

RaGOO is no longer supported. Please use RagTag instead: https://github.com/malonge/RagTag

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Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.

MitoZ: A toolkit for assembly, annotation, and visualization of animal mitochondrial genomes

De novo genome assembly and multisample variant calling

A bioinformatic toolkit to align genome assemblies into pangenome graphs

Compacted and colored de Bruijn graph construction and querying

Repeat-aware polishing genomes assembled using HiFi long reads

Long-reads Gap-free Chromosome-scale Assembler

A fast tool for hybrid genome assembly of long and short reads

Detailed bioinformatics scripts and methods used in the NAM genome paper.

Learning to untangle genome assembly with graph neural networks.