Read Threading

The thread command error corrects reads so they match the graph, then uses sequences that match the graph to generate links. Links connect kmers across collapsed repeats and allow us to traverse through them. If a read does not span any repeats, it will not generate any links.

Before running the thread command, you should run the inferedges command on the graph.

If you only want to error correct reads to match the graph, you can use the McCortex correct command.