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What is an optical map ?

Hello everybody.

After several research I still don't understand what is an optical map.

1) This figure confuse me because it looks like the output of the optical map are sequences ?

https://upload.wikimedia.org/wikipedia/commons/thumb/e/e1/Optical_mapping.jpg/1000px-Optical_mapping.jpg

2) And we can use it to make a de novo assembly ?

3) In that case, what is the advantage compared to long read data (like pacbio).

Thanks a lot for your explanations.

assembly optical map scaffold
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written by Picasa Picasa
  • Optical mapping technology is described in Bionano Genomics's page here.
  • Yes you can use optical mapping to create de novo assemblies (ref link above).
  • You are able to map over areas that are several hundred megabases long (almost chromosome size) which is currently not possible with PacBio. Long range structural variations/rearrangements can only be detected by Bionano like technology.
• 1 views • link
written by GenoMax GenoMax

Thanks for your link.

1 ) So can we say that Bionano optical map tend to replace Long reads sequencing (Pacbio and nanopore) ?.

2) I am not sure to understand what is the output of Bionano: raw reads ? if yes, what is the error rate ?

• 1 views • link
written by Picasa Picasa

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