zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)

Illumina short read assembly data pipeline for phage

Nanopore long read assembly data pipeline for phage genomes

PHANOTATE: a tool to annotate phage genomes.

codoff: a program to measure the irregularity of the codon usage for a single genomic region (e.g. a BGC, phage, etc.) relative to the full genome.

code repo for mobileOG-db

Configurable short read de novo assembly container using SPAdes and bbmap

PhageOrder is a python package designed to reorder phage genomes based on its terminase subunit.

Scripts to analyze the data for the paper "An outstanding bacterial membranome requires CRISPR-Cas systems to avoid the intervention of phages" and derive the figures or subfigures shown in the manuscript.

A toy MC model studying bacteria-phage coevolution dynamics. Code is meant to be readable instead of performant, or, well, good. Good for beginners in ABM

Report, proposal, and mvp implementation of a simple tool for use in finding motifs in genome data. 🧬

This is the complete code base used in Robert A. Edwards, Katelyn McNair, Karoline Faust, Jeroen Raes, and Bas E. Dutilh (2015) Computational approaches to predict bacteriophage–host relationships. FEMS Microbiology Reviews doi: 10.1093/femsre/fuv048

iGEM 19 Synthetic Biology

A powerful deep learning (DL) tool and the trained models for the phage gene and protein identification with convolutional neural network (CNN).