Concatenating multiple graphs

Concatenating multiple assembly graphs

agtools can concatenate multiple GFA files. This can be useful for downstream analysis of assemblies with multiple samples. You can use the concat subcommand provided through the command-line interface. Please refer to the CLI reference for further details on the concat subcommand.

Note

The concat subcommand will NOT merge similar segments. It simply concatenates the segments and other elements in the GFA files.

You can run the following command to concatenate multiple GFA files. Make sure to provide each GFA file using -g.

agtools concat -g test_graph_1.gfa -g test_graph_2.gfa -g test_graph_3.gfa -o results/concatenated_graph.gfa

The lines with the tags H, S, L, J, C, P, and W will be grouped across the input GFA files and written together.

Tip

If two GFA files have the same segment ID, path ID or walk ID, the run will fail. If you have duplicate IDs, please make sure to run the rename subcommand before concatenating.