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
Lu CL, Chen KT, Huang SY, Chiu HT "CAR: contig assembly of prokaryotic draft genomes using rearrangements." BMC Bioinformatics. 2014 Nov 28;15:381. https://doi.org/10.1186/s12859-014-0381-3
PMID: 25431302
PMCID: PMC4253983
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