GFA Retrieve and Bandage Diagram — Hybrid Assembly Viewer

What does it do?

Use GFA Retrieve to obtain Graphical Fragment Assembly (.gfa) files produced by the hybrid assembly pipeline. A GFA file represents assembly-graph connections that are not visible in a standard contig FASTA file.

Use Bandage to draw and inspect the graph. The graph can help identify simple, well-resolved assemblies and complex assemblies that may need further investigation.

Only the hybrid assembly pipeline currently produces GFA files, so requests should use MIN identifiers in the form YYYY-MIN-NNNN.

How do I use it?

Subject

In the Subject field, enter:

gfaretrieve

Description

In the Description field, enter one hybrid-assembly SEQID per line:

2026-MIN-0001
2026-MIN-0002

Older MIN assemblies may not have a GFA file if they were created before the pipeline produced this output.

Attachments

No attachment is required. GFA Retrieve locates the graph file associated with each requested hybrid assembly.

Optional parameters

The supplied documentation does not identify optional parameters for GFA Retrieve.

Example

2026-MIN-0001
2026-MIN-0002

See issue 33691 for an example GFA Retrieve request.

Interpreting results

Open each .gfa file in Bandage to visualize the assembly graph.

A simple graph with a small number of separate components can be consistent with a well-resolved hybrid assembly. For example, one large component may represent the chromosome and smaller components may represent plasmids. Graph structure alone is not definitive proof of chromosome or plasmid identity.

A tangled graph with many components or unresolved connections can indicate a complex or problematic assembly. Potential causes include incorrect read pairing, contamination, repeated regions, insufficient data, or combining Illumina and Nanopore reads from different isolates. Review the source data and consult a bioinformatician before drawing conclusions.

Download and open Bandage

Bandage can currently be downloaded and used on corporate Windows laptops. Additional tools integrated with Bandage, such as BLAST, may not be available in that environment.

  1. Go to the Bandage website.
  2. Select Download Windows.
  3. Extract the downloaded ZIP archive.
  4. Open the extracted Bandage folder.
  5. Double-click Bandage.exe.

The initial interface should resemble:

Bandage graphical user interface

To load and draw a graph:

  1. Select File → Load graph.
  2. Choose the .gfa file.
  3. After the file loads, select Draw graph in the Graph drawing panel.

A loaded graph should resemble:

Bandage with a loaded GFA graph

Example of a simple hybrid assembly graph

The following example is 2024-MIN-0073, a Klebsiella hybrid assembly with three separate components. These may represent one chromosome and two plasmids.

Example of a simple hybrid assembly graph

Example of a problematic hybrid assembly graph

The following example used Illumina reads from an Acinetobacter isolate with Nanopore reads from a Klebsiella isolate. The resulting graph contains 93 contigs and is difficult to interpret.

Example of a problematic hybrid assembly graph

If a graph resembles this example, verify that the Illumina and Nanopore reads came from the same isolate and discuss the assembly with a bioinformatician.

For additional instructions, see the Bandage getting-started tutorial.

How long does it take?

GFA retrieval time depends on the number of requested SEQIDs, file availability, and current service workload.

What can go wrong?

A requested SEQID is unavailable

Symptom: The Redmine issue receives a warning identifying unavailable sequences or graph files.

Likely cause: The SEQID is incorrect, the hybrid assembly is unavailable, or the assembly has no GFA output.

What to do: Verify the SEQID and confirm that it is a hybrid YYYY-MIN-NNNN assembly.

An older MIN assembly has no GFA file

Symptom: The assembly exists, but GFA Retrieve cannot return a graph file.

Likely cause: The assembly was generated before the hybrid pipeline produced GFA files.

What to do: Consult a bioinformatician to determine whether the graph can be regenerated.

Bandage cannot use an integrated BLAST function

Symptom: Bandage opens and draws a graph, but an additional BLAST-dependent feature does not work on the corporate Windows device.

Likely cause: The supporting BLAST programs are not available in the corporate Windows environment.

What to do: Use Bandage for graph visualization and consult a bioinformatician if BLAST-assisted graph analysis is required.

The graph is highly fragmented or tangled

Symptom: Bandage shows many components or complex unresolved connections.

Likely cause: The assembly may contain mismatched reads, contamination, repeated regions, insufficient data, or another assembly-quality issue.

What to do: Verify that the Illumina and Nanopore reads belong to the same isolate, review sequence quality, and consult a bioinformatician.

  • SequenceExtractor — extracts a nucleotide interval or complete contig from an assembly.
  • MobSuite — predicts plasmid-derived contigs and performs plasmid typing in draft genome assemblies.