A pipeline for identification and annotation of transposable element (TE) insertions using next generation sequencing (NGS) data.
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Updated
Aug 5, 2021 - Python
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
Detect elevations and gaps in read coverage on metagenome contigs or assembled genomes
Tn3 Transposon/Toxin Finder
Composite Transposon Finder
skandiver is a program for identifying mobile genetic elements (prophages, plasmids, transposases, etc.) from assembled whole genome sequences using average nucleotide identity (ANI)
A reference-free statistical approach to diversity-generating & mobile genetic element discovery
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.
Tool intended to pull out sequences and annotations between insertion sites specified by the user.
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
code repo for mobileOG-db
zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)
Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.
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