mobile-genetic-elements

Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.

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

code repo for mobileOG-db

AMR/VF LGT focused bacterial genomics analysis workflow

An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences

skandiver is a program for identifying mobile genetic elements (prophages, plasmids, transposases, etc.) from assembled whole genome sequences using average nucleotide identity (ANI)

Tool intended to pull out sequences and annotations between insertion sites specified by the user.

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

Snakemake workflow for bacterial whole-genome sequencing: assembly, QC, taxonomy, annotation, AMR and virulence, plasmids and prophages — plus an optional mobilome module that reports whether each AMR gene sits in a mobile element and how transferable it is. Four entry points: Illumina, Nanopore, hybrid or assembled contigs.

Composite Transposon Finder

A reference-free statistical approach to diversity-generating & mobile genetic element discovery

Tn3 Transposon/Toxin Finder

An interactive and user-friendly web application to explore the hospital microbiome and genetic makeup

Automated detection of unfixed mobile genetic elements in long read DNA sequencing data

Detect elevations and gaps in read coverage on metagenome contigs or assembled genomes

Curated genomic database of Staphylococcus plasmids, mobile genetic elements that contribute to bacterial adaptation and pathogenicity through horizontal gene transfer. These elements may carry virulence factors, including enterotoxins, as well as antimicrobial resistance genes and other adaptive traits.

An R shiny application to explore the chicken gut microbiome and their genetic makeup

Metabundance: Investigating ARG abundance in metagenomes and linking them to MGEs

Curated genomic database of Staphylococcal Pathogenicity Islands (SaPIs), mobile genetic elements in Staphylococcus aureus that contribute to virulence through carriage of enterotoxin and other virulence-associated genes.

A pipeline for identification and annotation of transposable element (TE) insertions using next generation sequencing (NGS) data.