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 304 fly genomes.

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.

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

Comprehensive in-silico subunit vaccine discovery workflow

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

Scripts used by George S. Long

Genomics Part of the KAUST High Throughput Sequencing Workshop 2019

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

Aphrocallistes vastus genome

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

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

Workshops, Course Schedule and Teaching Assistant Review from my time as a chosen Undergraduate Teaching Assistant for the University of Pittsburgh course, BIOSC1540 - Computational Genomics taught by Dr. Miler Lee.

Comprehensive three-way consensus annotation pipeline for Giardia genomes (v5.0)