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

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

AMR/VF LGT focused bacterial genomics analysis workflow

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.

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

code repo for mobileOG-db

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

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

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

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

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

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

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

Composite Transposon Finder

Tn3 Transposon/Toxin Finder