Mobilome annotation pipeline (MAP)

Description of mobilome annotation in the MGnify assembly analysis.

Author

Affiliation

MGnify

EMBL-EBI

The Mobilome Annotation Pipeline (MAP) is a separate pipeline run after the assembly annotation pipeline. It is one of the three pipelines of the assembly analysis. It integrates the prediction and annotation of mobile genetic elements (MGE) and generates final results in GFF3 format. VIRify results are incorporated into the mobilome annotation.

Results available on MGnify

For each analysed assembly, MGnify displays and provides downloads for:

• The integrated MGE annotations in GFF3 format.
• A FASTA file with the sequence records for all predicted mobile genetic elements.

Technical details and results reference

Tools used

Tool	Version	Purpose
geNomad	1.11.1	Plasmid and phage prediction
ICEfinder2-lite refactored from ICEfinder2	2.0	Detection of integrative conjugative and mobilisable elements
IntegronFinder2	2.0.6	Integron identification
ISEScan	1.7.3	Insertion sequence detection
Compositional Outliers	1.0	Non-autonomous MGEs detection based on sequence composition

Reference databases

Reference Database	Version	Purpose
geNomad database	1.9	Reference database for plasmid and phage prediction
ICEfinder2 databases	N/A	MacSyFinder models, HMM models, and UniProt reference sequences

See Downloading databases in the MAP documentation for the full list of databases.

Pipeline workflow

1. Preprocessing: Contig filtering. MAP uses the protein-coding sequences predicted by the assembly annotation pipeline
2. Prediction: Concurrent execution of geNomad, ICEfinder2-lite, IntegronFinder2, and ISEScan, plus compositional outlier detection for contigs >100 kb
3. Integration: Results parsing and incorporation of VIRify output; fragments <500 bp and elements lacking genes are filtered out
4. Postprocessing: GFF validation and output compression

See the Mobilome annotation pipeline repository for detailed documentation.