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

SARS-CoV-2 Genome Assembler

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

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

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

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

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.

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

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.

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

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

Patch for LRSDAY v1.6 for Debian-based and SUSE-based OS.

Workflow to run Diploidocus on Setonix

Genomics Part of the KAUST High Throughput Sequencing Workshop 2019

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

example genomics workflow for student training

Scripts used by George S. Long