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CAR is a tool to rearrange contigs based on a known reference sequence. The algorithm implemented considers permutation of the contig groups and join them to match the reference. It is only implemented as a web application and only small prokaryotic genome can be scaffolded this way.


Reference-based scaffolding


  • Operation: Reference-based scaffolding
  • Input: FASTA
  • Output: FASTA
  • Software interface: Web user interface
  • Language: PHP
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: GNU GPL
  • Cost: Free
  • Version name: -
  • Credit: National Science Council of Taiwan
  • Contact: cllu _at_
  • Collection: -


Lu CL, Chen KT, Huang SY, Chiu HT "CAR: contig assembly of prokaryotic draft genomes using rearrangements." BMC Bioinformatics. 2014 Nov 28;15:381.
PMID: 25431302
PMCID: PMC4253983

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