In this GitHub Issue, Steven had suggested I try out the minimap/miniasm/racon pipeline for assembling our Olympia oyster PacBio data.
I followed the pipeline described by this paper: http://matzlab.weebly.com/uploads/7/6/2/2/76229469/racon.pdf.
This notebook entry just contains the racon execution. This produced this assembly:
All intermediate files generated from this pipeline are here:
I’ll put together a TL;DR post that provides an overview of the pipeline and an assessment of the final assembly.
Jupyter Notebook (GitHub): 20170918_docker_pacbio_oly_racon0.5.0.ipynb