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

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

AMR/VF LGT focused bacterial genomics analysis workflow

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, phage, etc.) relative to the full genome.

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

Composite Transposon Finder

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

Tn3 Transposon/Toxin Finder

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

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

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

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

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