Answers.Body: <p>PacBio and ONT are very different technologies; it would be helpful to be more specific. Regardless, I can only give my understanding as it relates to ONT reads....</p>
  <p>TLDR: use <a href="https://github.com/nanoporetech/medaka" rel="nofollow noreferrer">medaka</a>. Don't use Illumina reads.</p>
  <p>Nanopore reads called using the most recent super-accuracy basecallers have a very high consensus accuracy (q40-q50) for SNPs and non-homopolymeric INDELs after nanopore-only correction. ONT provide their own tool, <a href="https://github.com/nanoporetech/medaka" rel="nofollow noreferrer">medaka</a>, which uses assembly-mapped nanopore reads to correct the assembly. Medaka uses the base calling model from Guppy to predict the most likely sequence, given the input reads and the assembly.</p>
  <p>If you're using Illumina reads to polish a nanopore assembly, it should <em>only</em> be used to correct INDEL errors (and ideally, only homopolymer errors). The two most commonly-used tools that can correct nanopore reads using Illumina reads are <a href="https://github.com/lbcb-sci/racon" rel="nofollow noreferrer">Racon</a> and <a href="https://github.com/broadinstitute/pilon/wiki" rel="nofollow noreferrer">Pilon</a>. Based on the recency of the commit histories, I'd guess that Racon would be the most likely to work well. It looks like Racon can do both assembly correction <em>and</em> read correction.</p>
  
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Answers.CreationDate: 2021-12-02T02:38:41.857Z
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Answers.UserDisplayName: gringer
Answers.Body: <p>Why don’t you use a hybrid assembly which pretty much does it by default? Tools like OPERA-MS assemble the short reads with MEGAHIT and then uses nanopore to build bigger contgs. Otherwise, I recommend pilon which probably the most popular tool.</p>
  
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Answers.CreationDate: 2021-12-05T00:17:33.427Z
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Answers.UserDisplayName: Avamys
Answers.Body: <p>For PacBio HiFi reads (or other techs of comparable quality), it is not recommended to polish with Illumina at all. You run the risk of collapsing true heterozygosity/variation in your underlying genome and yielding a haploid assembly that does not represent either haplotype.</p>
  <p>If that underlying variation is an issue because you need a haploid assembly, you are free to use a deduplication technique such as purge_haplotigs or similar (<a href="https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-04118-3" rel="nofollow noreferrer">reviewed here</a>) to obtain a primary set of contigs/scaffolds. Assigning p and q haplotypes is something that you can do with a tool like <a href="https://www.google.com/url?sa=t&amp;rct=j&amp;q=&amp;esrc=s&amp;source=web&amp;cd=&amp;cad=rja&amp;uact=8&amp;ved=2ahUKEwiLufiHt7aDAxUwLTQIHYn0DAIQFnoECBAQAQ&amp;url=https%3A%2F%2Fgithub.com%2Fphasegenomics%2FFALCON-Phase&amp;usg=AOvVaw2ttek6UsNItYU1dATDadlW&amp;opi=89978449" rel="nofollow noreferrer">falcon-phase</a> (if you have Hi-C) or a similar technique (I haven't been following the literature for a couple years, possibly there's something a lot better now!).</p>
  <p>For a recent review of recommended strategies you can read <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9812399/" rel="nofollow noreferrer">the T2T consortium benchmarking paper on the topic</a>.</p>
  
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Answers.CreationDate: 2023-12-30T05:33:31.300Z
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Answers.UserDisplayName: Maximilian Press
Body: <p>Which tool would be good to polish PacBio or ONT with Illumina?</p>
  <p>Thank you in advance</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-12-01T14:38:53.593Z
Comments.Text: Do you mean to correct PacBio/ONT reads or polish their assembly?
Comments.UserDisplayName: user172818
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-12-30T05:24:12.217Z
Comments.Text: Metagenomic or single genome?
Comments.UserDisplayName: Maximilian Press
Tags: <nanopore><illumina><pacbio>
Title: Polishing PacBio or ONT with Illumina
ThreadText: # Polishing PacBio or ONT with Illumina
  
  (Asked by: username_0 on 2021-12-01)
  
  Which tool would be good to polish PacBio or ONT with Illumina?
  
  Thank you in advance
  
  **Tags:** nanopore, illumina, pacbio
  
  > **Comments:**
  > **username_1**: Do you mean to correct PacBio/ONT reads or polish their assembly?  
  > **username_2**: Metagenomic or single genome?  
  
  ---
  
  ## 3 answers
  
  ### Answer by username_3 on 2021-12-02. Score: 1
  
  PacBio and ONT are very different technologies; it would be helpful to be more specific. Regardless, I can only give my understanding as it relates to ONT reads....
  
  TLDR: use [medaka](https://github.com/nanoporetech/medaka). Don't use Illumina reads.
  
  Nanopore reads called using the most recent super-accuracy basecallers have a very high consensus accuracy (q40-q50) for SNPs and non-homopolymeric INDELs after nanopore-only correction. ONT provide their own tool, [medaka](https://github.com/nanoporetech/medaka), which uses assembly-mapped nanopore reads to correct the assembly. Medaka uses the base calling model from Guppy to predict the most likely sequence, given the input reads and the assembly.
  
  If you're using Illumina reads to polish a nanopore assembly, it should *only* be used to correct INDEL errors (and ideally, only homopolymer errors). The two most commonly-used tools that can correct nanopore reads using Illumina reads are [Racon](https://github.com/lbcb-sci/racon) and [Pilon](https://github.com/broadinstitute/pilon/wiki). Based on the recency of the commit histories, I'd guess that Racon would be the most likely to work well. It looks like Racon can do both assembly correction *and* read correction.
  
  
  ---
  
  ### Answer by username_4 on 2021-12-05. Score: 1
  
  Why don’t you use a hybrid assembly which pretty much does it by default? Tools like OPERA-MS assemble the short reads with MEGAHIT and then uses nanopore to build bigger contgs. Otherwise, I recommend pilon which probably the most popular tool.
  
  
  ---
  
  ### Answer by username_2 on 2023-12-30. Score: 0
  
  For PacBio HiFi reads (or other techs of comparable quality), it is not recommended to polish with Illumina at all. You run the risk of collapsing true heterozygosity/variation in your underlying genome and yielding a haploid assembly that does not represent either haplotype.
  
  If that underlying variation is an issue because you need a haploid assembly, you are free to use a deduplication technique such as purge\_haplotigs or similar ([reviewed here](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-04118-3)) to obtain a primary set of contigs/scaffolds. Assigning p and q haplotypes is something that you can do with a tool like [falcon-phase](https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&cad=rja&uact=8&ved=2ahUKEwiLufiHt7aDAxUwLTQIHYn0DAIQFnoECBAQAQ&url=https%3A%2F%2Fgithub.com%2Fphasegenomics%2FFALCON-Phase&usg=AOvVaw2ttek6UsNItYU1dATDadlW&opi=89978449) (if you have Hi-C) or a similar technique (I haven't been following the literature for a couple years, possibly there's something a lot better now!).
  
  For a recent review of recommended strategies you can read [the T2T consortium benchmarking paper on the topic](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9812399/).
  
  
  ---
  
  