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: https://matzlab.weebly.com/uploads/7/6/2/2/76229469/racon.pdf.

This notebook entry just contains the racon execution. This produced this assembly:

https://owl.fish.washington.edu/Athaliana/201709_oly_pacbio_assembly_minimap_asm_racon/20170918_oly_pacbio_racon1_consensus.fasta

All intermediate files generated from this pipeline are here:

https://owl.fish.washington.edu/Athaliana/201709_oly_pacbio_assembly_minimap_asm_racon/

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