<p>Nanopolish is necessary if you want to get high-quality consensus. racon etc don't use signal data. They can't achieve high quality. pilon at times doesn't work well. Even if it worked perfectly, it wouldn't help repetitive regions inaccessible by short reads.</p>

CC BY-SA 4.0
2019-03-05T18:44:58.817Z
You're quite right. I polished twice with racon then twice with pilon. Mapped short read pairs and long reads. All of the gaps in the short read mappings were covered with long reads. Going to use nanopolish now!
conchoecia
CC BY-SA 4.0
2019-03-03T14:44:19.827Z
2019-03-03T14:44:19.827Z
user172818
<p>For Oxford Nanopore contigs produced by any long-read assembler has anyone performed any benchmarks to compare the polishing tools <a href="https://github.com/isovic/racon" rel="nofollow noreferrer"><code>racon</code></a>, <a href="https://github.com/jts/nanopolish" rel="nofollow noreferrer"><code>nanopolish</code></a>, or something like <a href="https://github.com/ruanjue/wtdbg2" rel="nofollow noreferrer"><code>wtpoa-cns</code></a>?</p>

<p>The compute time of <code>nanopolish</code> is quite long and I would rather use another tool if it will suffice. After long-read polishing I will polish more with two rounds of <a href="https://github.com/broadinstitute/pilon" rel="nofollow noreferrer"><code>pilon</code></a> using 200x coverage Illumina shotgun data from the same individual.</p>

<nanopore><assembly><long-reads>
Is nanopolish worth it since faster polishing software is available?
# Is nanopolish worth it since faster polishing software is available?

(Asked by: username_0 on 2019-03-02)

For Oxford Nanopore contigs produced by any long-read assembler has anyone performed any benchmarks to compare the polishing tools [`racon`](https://github.com/isovic/racon), [`nanopolish`](https://github.com/jts/nanopolish), or something like [`wtpoa-cns`](https://github.com/ruanjue/wtdbg2)?

The compute time of `nanopolish` is quite long and I would rather use another tool if it will suffice. After long-read polishing I will polish more with two rounds of [`pilon`](https://github.com/broadinstitute/pilon) using 200x coverage Illumina shotgun data from the same individual.

**Tags:** nanopore, assembly, long-reads

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## 1 answers

### Answer by username_1 on 2019-03-03. Score: 3 | Accepted answer

Nanopolish is necessary if you want to get high-quality consensus. racon etc don't use signal data. They can't achieve high quality. pilon at times doesn't work well. Even if it worked perfectly, it wouldn't help repetitive regions inaccessible by short reads.

> **Comments:**
> **username_0**: You're quite right. I polished twice with racon then twice with pilon. Mapped short read pairs and long reads. All of the gaps in the short read mappings were covered with long reads. Going to use nanopolish now!  

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