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.

Paired end reads that overlap should also be merged in order to give the most information. The read threading steps attempts to error correct reads and fill in insert gaps, but it cannot merge overlapping reads. Instead there are many good tools for this. We considered implementing this functionality ourselves, but want to avoid "re-inventing the wheel" and would likely not perform as well as existing solutions. We suggest using FLASH, COPE, PEAR or PANDASeq.

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