<![CDATA[BOL: repeat-aware: Repeat aware scaffolding evaluation framework by Igor Mandric]]> https://bioinformaticsonline.com/bookmarks/view/36015/repeat-aware-repeat-aware-scaffolding-evaluation-framework-by-igor-mandric? https://bioinformaticsonline.com/bookmarks/view/36015/repeat-aware-repeat-aware-scaffolding-evaluation-framework-by-igor-mandric Wed, 21 Mar 2018 18:10:00 -0500 https://bioinformaticsonline.com/bookmarks/view/36015/repeat-aware-repeat-aware-scaffolding-evaluation-framework-by-igor-mandric <![CDATA[repeat-aware: Repeat aware scaffolding evaluation framework by Igor Mandric]]> Genome scaffolding is a classical challenging problem in bioinformatics. It refers to joining assembly contigs into chains (called scaffolds). The join between two contigs A and B is considered correct if:

  • Their relative orientation is correct
  • Their relative order is correct
  • The gap estimate is similar to the true distance on the reference

The problem of scaffolding validation is also a challenging one. One of the main issues which hinders from an adequate scaffolding evaluation are genome repeats. The previous standard for evaluation (Hunt et al., Genome Biology, 2014) did not take into account repeats. In this evaluation framework, repeats are taken into account.

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The new evaluation framework considers the optimal assignment of contigs in the output scaffolding to contigs in the reference scaffolding in the sense of the number of correct links.

 

https://github.com/mandricigor/repeat-aware

Address of the bookmark: https://github.com/mandricigor/repeat-aware

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