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

A pipeline for viral identification from metagenomic samples

Detecting transposable element invasions without repeat library. Detects also horizontal transfer events and endogenized viruses. All you need is a reference genome and some short reads

Generate statistics from FASTQ and FASTA files. Also manipulate sequences such as renaming/sorting contigs and converting FASTQ to FASTA. Written in Bash. All in one place.

SARS-CoV-2 Genome Assembler

Fully automatic k-mer based polishing for genome assemblies. Based on original concept and design from Ivan Sovic, Ann McCartney, and Arang Rhie

PAQman is a tool for a reference-free and comprehensive evaluation of genome assemblies

VIPER is a user-friendly software for assembling and identifying viral genomes (currently SARS-CoV-2, Dengue, and Influenza), from Illumina sequencing data generated through genomic surveillance.

Analysis workflow to generate fungal assemblies, generate gene structural and functional annotations

Automatically and reproducibly runs Autocycler (v. 0.4.0) with additional long-read QC, assembly reorientation, and optional short-read QC and polishing.

Teaching Material for Course "Computational Bioscience & Machine Learning 2021 - Genome Assembly"

Scripts and notes related to the manuscript: Stuart KC & Edwards RJ et al. 2022. Transcript- and annotation-guided genome assembly of the European starling. Molecular Ecology Resources, doi.org/10.1101/2021.04.07.438753. † joint first author

fusemblr is a pipeline wrapper designed for the assembly of complex genomes using nanopore reads and paired-end illumina

Fast microbial species identification (16S rRNA gene-based approach) and contamination check using whole genome assemblies

This is a template for all assembly projects. Please read the instructions below on how to use it.

Jonah Crab, once considered bycatch in the lobster industry, are now one of the most valuable fisheries in Massachusetts. A chromosome-level reference genome was generated to enable lcWGS population structure assessment

Polap is a plant mtDNA assembly pipeline using Flye long-read assembler guided by organelle gene annotation.

This repository contains the main codes used in the manuscript: "Oryza genome evolution through a tetraploid lens"

De novo genome assembly of subset of the durian fruit genome.

Scripts for Hill et al. (2023) doi:10.1093/gbe/evad038 🌿