MobSuite

What does it do?

Use MobSuite to detect, reconstruct, and type predicted plasmids in draft genome assemblies.

The Redmine automator runs the mob_recon component of MOB-suite. mob_recon assigns assembly contigs to predicted chromosome or plasmid groups and provides typing information for reconstructed plasmids.

MOB-suite was developed by the Public Health Agency of Canada. For method details and complete output definitions, see the MOB-suite repository.

How do I use it?

Subject

In the Subject field, enter:

MobSuite

Spelling matters, but matching is not case-sensitive.

Description

Enter one draft-assembly SEQID per line:

2026-SEQ-0001
2026-SEQ-0002

Attachments

No attachment is required. MobSuite retrieves the draft genome assembly associated with each requested SEQID.

Optional parameters

The supplied documentation does not identify optional parameters for the Redmine MobSuite automator.

Example

See issue 37387 for an example MobSuite request.

Interpreting results

MobSuite uploads a ZIP archive containing one directory for each requested SEQID. Each directory contains the MOB-suite output for that assembly.

An important output is:

contig_report.txt

This report assigns each assembly contig to a predicted chromosome or plasmid group and includes typing information for plasmid-derived contigs.

Plasmid reconstruction from a draft assembly is predictive. One plasmid may be represented by several contigs, repeated regions can complicate reconstruction, and chromosomal or plasmid assignments should be interpreted with assembly quality and supporting evidence.

See the MOB-suite repository for definitions of all other output files and columns.

How long does it take?

MobSuite generally takes approximately one minute per requested SEQID. Total runtime depends on assembly size, sample count, compute availability, and result-upload time.

What can go wrong?

A requested SEQID is unavailable

Symptom: The Redmine issue receives a warning identifying unavailable assemblies.

Likely cause: MobSuite cannot locate the draft assembly associated with the requested SEQID.

What to do: Verify each SEQID, confirm that its assembly exists, and submit a corrected request.

The Dropbox upload times out

Symptom: The analysis may complete, but the issue reports an upload error or does not provide a usable result link.

Likely cause: The Dropbox upload timed out or encountered a temporary connection problem.

What to do: Retry later if the problem is transient. If it persists, contact the bioinformatics team with the Redmine issue number.

A plasmid prediction is uncertain

Symptom: A predicted plasmid is fragmented across several contigs or a contig assignment is difficult to interpret.

Likely cause: The draft assembly is fragmented, contains repeated sequence, or lacks enough context for unambiguous reconstruction.

What to do: Review contig_report.txt, assembly quality, and other MOB-suite outputs together. Use long-read or hybrid assembly evidence when available.

  • AMRsummary — combines ResFinder acquired-AMR results with MOB-suite plasmid-location predictions.
  • Plasmid-Borne Identity — searches assemblies for user-supplied targets and predicts whether matching targets are plasmid-borne.
  • PHASTEST — detects prophage regions in assembled bacterial genomes. Use MobSuite for predicted plasmids and PHASTEST for prophages when both types of mobile genetic element must be investigated.