DEPRECATED: Use Cenote-Taker 3 instead

Donut: automated Circos visualization of multiple fasta files within a docker image

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

SLURM-ready bash scripts to run the complete REPET pipeline

A comparative annotation toolkit (CAT) pipeline for 301 Drosophila genomes.

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

A Dockerfile and associated tools for deploying containerized InterProScan5.

SmedAnno is a robust RNA-Seq annotation pipeline designed to streamline analysis from raw reads to a comprehensive, functionally annotated gene set. It handles short reads, long reads, or a combination of both, and provides extensive quality control metrics to help identify potentially fragmented or chimeric gene models.

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

Comprehensive in-silico subunit vaccine discovery workflow

This repository houses the scripts for my contribution to the global durum wheat pangenome project.

Scripts used by George S. Long

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

Aphrocallistes vastus genome

Genomics Part of the KAUST High Throughput Sequencing Workshop 2019

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

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

This is the repository containing the scripts and tutorials for running the bagRNA genome annotation pipeline