Racon polishing script that maps long reads and does racon polishing continuously until no changes are seen

Question

[zack.saud]

Has anyone come across a script that does that maps long reads and does racon polishing continuously until no changes are seen? I have Nanopore Long reads and it takes a long time to manually map and then invoke racon. I know the Unicycler assembler had a built in function to racon polish until no further changes were seen, but does anyone have a script that does just that automatically?

Many thanks

Answer 1

[colindaven]

Not exactly what you asked, but a student of mine created a simple pipeline which does two rounds of minimap2/racon followed by medaka.

https://github.com/Colorstorm/assembly_polishing_racon_medaka/blob/master/run_polish_pipe_SLURM.sh