Answers.Body: <p><strong>Disclaimer</strong>, this answer is based on feeling I got from talks and papers, but I do not have any hard reference supporting it.</p>
  
  <p>I believe that genome polishing is a technique that was introduced for correction of individual bases of long noisy read assemblies - i.e. fixing SNPs and short indels. Guessing a correct base from long reads during assembly seems to be bit more complicated task in comparison to short read assemblies, therefore it is isolated into separated algorithms like <a href="https://github.com/PacificBiosciences/unanimity" rel="noreferrer">Quiver/Arrow</a>, <a href="https://github.com/jts/nanopolish" rel="noreferrer">Nanopolish</a> (for correction by long reads) or the tool you mentioned - <a href="https://github.com/broadinstitute/pilon/wiki" rel="noreferrer">Pilon</a> (correction by short reads).</p>
  
  <p>Miss-assemblies could be corrected even prior long reads for instance by matching the assembly to optical mapping, or by tools like <a href="https://www.sanger.ac.uk/science/tools/reapr" rel="noreferrer">REAPR</a> or <a href="https://github.com/ksanao/TGNet" rel="noreferrer">TGnet</a>. However, I have never heard term "genome polishing" used for this type of genome correction.</p>
  
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Answers.CreationDate: 2018-05-15T21:21:13.363Z
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Answers.UserDisplayName: Kamil S Jaron
Answers.Body: <p>In long-read assembly, "polish" refers to the step to improve the base accuracy of contig sequences. I believe the terminology was originated from the <a href="https://www.ncbi.nlm.nih.gov/pubmed/23644548" rel="noreferrer">HGAP paper</a>:</p>
  
  <blockquote>
    <p>The final consensus–calling algorithm Quiver, which takes into account all of the underlying data and the raw quality values inherent to SMRT sequencing, then <strong><em>polishes</em></strong> the assembly for final consensus accuracies in excess of 99.999% (QV of >50)...</p>
  </blockquote>
  
  <p>Pilon was published more than a year later and in fact, neither its paper nor README mentions word "polish".</p>
  
  <p>By the way, "error correction" refers to the step to fix sequencing errors in raw reads, not in contigs. In Canu/HGAP/Falcon, that step is done by pbdagcon or falcon_sense.</p>
  
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Answers.UserDisplayName: user172818
Body: <ol>
  <li><p>Is there a standard definition for "assembly polishing" in the field? </p></li>
  <li><p>Is there a standard definition for what polishing algorithms do? </p></li>
  </ol>
  
  <p>My understanding of "polishing" is strongly influenced by <a href="https://github.com/broadinstitute/pilon/wiki" rel="nofollow noreferrer">Pilon</a>:</p>
  
  <p>Whereby users input a reference FASTA along with the BAM of aligned reads against this reference FASTA. The polishing algorithm then does alignment to discover local misassemblies and other alignment inconsistencies. These are then "corrected", i.e. "polished". </p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-05-15T20:29:34.667Z
Comments.Text: Anything that makes something more correct (or shinier) would be polishing it in English, there's no special meaning here.
Comments.UserDisplayName: Devon Ryan
Tags: <phylogenetics><assembly>
Title: Is there a standard definition for "assembly polishing"?
ThreadText: # Is there a standard definition for "assembly polishing"?
  
  (Asked by: username_0 on 2018-05-15)
  
  1. Is there a standard definition for "assembly polishing" in the field?
  2. Is there a standard definition for what polishing algorithms do?
  
  My understanding of "polishing" is strongly influenced by [Pilon](https://github.com/broadinstitute/pilon/wiki):
  
  Whereby users input a reference FASTA along with the BAM of aligned reads against this reference FASTA. The polishing algorithm then does alignment to discover local misassemblies and other alignment inconsistencies. These are then "corrected", i.e. "polished".
  
  **Tags:** phylogenetics, assembly
  
  > **Comments:**
  > **username_1**: Anything that makes something more correct (or shinier) would be polishing it in English, there's no special meaning here.  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_3 on 2018-05-16. Score: 6 | Accepted answer
  
  In long-read assembly, "polish" refers to the step to improve the base accuracy of contig sequences. I believe the terminology was originated from the [HGAP paper](https://www.ncbi.nlm.nih.gov/pubmed/23644548):
  
  > The final consensus–calling algorithm Quiver, which takes into account all of the underlying data and the raw quality values inherent to SMRT sequencing, then ***polishes*** the assembly for final consensus accuracies in excess of 99.999% (QV of >50)...
  
  Pilon was published more than a year later and in fact, neither its paper nor README mentions word "polish".
  
  By the way, "error correction" refers to the step to fix sequencing errors in raw reads, not in contigs. In Canu/HGAP/Falcon, that step is done by pbdagcon or falcon\_sense.
  
  
  ---
  
  ### Answer by username_2 on 2018-05-15. Score: 5
  
  **Disclaimer**, this answer is based on feeling I got from talks and papers, but I do not have any hard reference supporting it.
  
  I believe that genome polishing is a technique that was introduced for correction of individual bases of long noisy read assemblies - i.e. fixing SNPs and short indels. Guessing a correct base from long reads during assembly seems to be bit more complicated task in comparison to short read assemblies, therefore it is isolated into separated algorithms like [Quiver/Arrow](https://github.com/PacificBiosciences/unanimity), [Nanopolish](https://github.com/jts/nanopolish) (for correction by long reads) or the tool you mentioned - [Pilon](https://github.com/broadinstitute/pilon/wiki) (correction by short reads).
  
  Miss-assemblies could be corrected even prior long reads for instance by matching the assembly to optical mapping, or by tools like [REAPR](https://www.sanger.ac.uk/science/tools/reapr) or [TGnet](https://github.com/ksanao/TGNet). However, I have never heard term "genome polishing" used for this type of genome correction.
  
  
  ---
  
  