Genome Assembly - Olympia oyster PacBio minimap/miniasm/racon

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:

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.

Previously ran minimap and then miniasm.

Jupyter Notebook (GitHub): 20170918_docker_pacbio_oly_racon0.5.0.ipynb