genome-assembly

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

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

[THIS REPO IS DEPRECATED] see newer repos: https://github.com/broadinstitute/viral-core https://github.com/broadinstitute/viral-assemble https://github.com/broadinstitute/viral-phylo https://github.com/broadinstitute/viral-classify https://github.com/broadinstitute/viral-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

A program for assessing the T2T genome continuity

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