A genome alignment and visualization system

MFannot is a program for the annotation of mitochondrial and plastid genomes

GRAbB (Genome Region Assembly by Baiting) is a program designed to assemble selected regions of the genome or transcriptome using reference sequences and NGS data.

🌺 reference-free transcriptome assembly for short and long reads

OPERA-MS - Hybrid Metagenomic Assembler

Ultrafast de novo assembly for long noisy reads (though having no consensus step)

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

A gap-closing software tool that uses long reads to enhance genome assembly.

Use long transcriptome reads to scaffold genomes

An imagemagick-like frontend to Biopython SeqIO

Genie: A Fast and Robust Hierarchical Clustering Algorithm (this R package has now been superseded by genieclust)

Scripts and documentations on the MCSC decontamination method

Tools for fast and flexible genome assembly scaffolding and improvement

Minimizer-based assembly scaffolding and mapping using long reads

Implementation of ToL genome assembly workflows

BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eukaryotic genomes

Protein hint generation pipeline for gene finding in eukaryotic genomes

🔬 Assemble large genomes using short reads

TheBGAcademy 2024: Exploring Satellite DNA using ModDotPlot

TheBGAcademy 2024: Gene prediction with BRAKER3

TheBGAcademy 2024: Learn how to run verkko assembler as well as going over the different outputs and common things to check an assembly for first.

Tools (written in C using htslib) for manipulating next-generation sequencing data

an automated gap closing tool

De-Novo Repeat Discovery Tool

Eukaryotic Genome Annotation Pipeline

Hybird Scaffolding Tool

Correct and scaffold assemblies using long reads

Fast and accurately polish the genome generated by long reads.

RNA-seq aligner