racon

name	racon
description	Ultrafast consensus polishing of assemblies using mapped long (or short) reads. Use after long-read or hybrid assembly before binning/annotation. Upstream: https://github.com/lbcb-sci/racon.
license	MIT
category	analysis-tools
tags	["polish","assembly","long-read"]
upstream	https://github.com/lbcb-sci/racon
stage	assembly

Racon

Upstream: lbcb-sci/racon

Citation

Vaser, R., Sović, I., Nagarajan, N. & Šikić, M. Fast and accurate de novo genome assembly from long uncorrected reads. Genome Res. 27, 737–746 (2017). https://doi.org/10.1101/gr.214270.116

Analytical thinking

Racon polishes contigs given overlaps from mapping (usually Minimap2 PAF). Typical long-read loop: assemble → map reads → racon → (optional repeat). Do not expect Racon alone to fix massive mis-assemblies; it refines consensus.

For Illumina polishing of long-read drafts, consider pilon / Polypolish ecosystems as alternatives.

How to run

conda install -c bioconda racon minimap2

minimap2 -x map-ont -t 16 assembly.fa reads.fastq.gz > temp/polish/map.paf
racon -t 16 reads.fastq.gz temp/polish/map.paf assembly.fa \
  > temp/polish/assembly.racon.fa

Related skills

minimap2 · metaflye · metamdbg · pilon · quast