Sean’s Notebook: Canu running, figuring…

Sean’s Notebook: Canu running, figuring out Racon and what it needs next.

So I got Racon, a consensus caller installed, and it looks like it requires mapping position information. The Racon developers suggested Minimap for that purpose. I installed Minimap on Emu so I could run it on the filtered reads while Canu is running on Hyak.

It looks like the general process will be as follows

  • Canu to make preliminary contigs
  • Map Raw reads to contigs with Minimap
  • Consensus call with Racon
  • Repeat the above steps ~ 3 times (that seems to be a common number)
  • Map the raw Illumina reads to the final Racon output with samtools
  • Use Pilon to polish with the mapped .sam files.
  • End with an assembly based on PacBio reads, and finished with Illumina, the opposite of the Platanus/Redundans workflow.

We’re currently on step 1, so this might take a little while…