Ultra-fast and memory-efficient (meta-)genome assembler
Tools for fast and flexible genome assembly scaffolding and improvement
Fast and accurate de novo assembler for long reads
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.
Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets
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
Repeat-aware polishing genomes assembled using HiFi long reads
Compacted and colored de Bruijn graph construction and querying
Detailed bioinformatics scripts and methods used in the NAM genome paper.
Long-reads Gap-free Chromosome-scale Assembler
A fast tool for hybrid genome assembly of long and short reads
Simple bacterial assembly and annotation pipeline