Polishing Reads long or Short

Question

[midox]

Hello,

I want to know what that means "Polishing Reads"? And what is the utility of that?

Thank you

[Medhat]

I know assembly polishing and for that there is tools like Pilon or quiver; where did you read the "Polishing Reads" is it just mean trimming?

[midox]

Even in assembly! what's this?

Answer 1

[Medhat]

Polishing is trying to correct the errors/improve genome assembly from the technology used for example

Suppose you have assembled a genome, but suspect it has some minor errors. For example, it might have been assembled from 454 or IonTorrent reads and have homopolymer length errors. The assembly can then be polished using, say, an Illumina read set (higher quality but shorter).

or in case of long reads like PacBio or Nanopore which have high error rates you could use either self correction or correct with high fidelity reads like Illumina or any other technology

for tools I previously mentioned ( Pilon or quiver)

another meaning is to finish the genome and close gaps

Although computer programs can help resolve gaps and uncertainties in a genome sequence, much of the final polishing is still done by people known as finishers. These expert workers identify gaps in the sequence, design experiments to fill in those gaps, and determine how to collect any additional information that is necessary.

There is no mechanical substitute for the intuition and intelligence of an experienced finisher, so finishing is currently a bottleneck in the process of DNA sequencing. Automatic sequencing machines can churn out raw sequence much faster than humans can analyze and polish these sequences.