Configurable short read de novo assembly container using SPAdes and bbmap
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Updated
May 10, 2024 - Python
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.
Nanopore long read assembly data pipeline for phage genomes
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.
Illumina short read assembly data pipeline for phage
A powerful deep learning (DL) tool and the trained models for the phage gene and protein identification with convolutional neural network (CNN).
Report, proposal, and mvp implementation of a simple tool for use in finding motifs in genome data. 🧬
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
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.
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
code repo for mobileOG-db
zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)
PHANOTATE: a tool to annotate phage genomes.
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