Racon polishing script that maps long reads and does racon polishing continuously until no changes are seen
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14 months ago
zack.saud ▴ 40

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

sequencing assembly genome alignment • 935 views
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14 months ago
colindaven ★ 3.3k

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

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