| 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
