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Chimerism is a phenomenon in which the link in a read pair does not accurately describe the separation of the reads in the genome. Such a link is called a chimeric link, and the reads in the pair are called chimeric reads.

Chimerism often occurs in Sanger sequencing because clones are often accidentally merged together before sequencing. If two clones containing different regions of the genome are merged into a single insert, and that insert is then read at each end, the resulting read pair will be chimeric.

Chimerism becomes evident after reads are placed in an assembly. Chimeric reads may be much farther away from each other than their link suggests, or both oriented in the same direction. This leads to nonsensical insert sizes.

When Arachne definitively detects a chimeric read pair, it discards both reads, noting them in assembly.unplaced. As a further precaution against chimerism, Arachne will not merge two supercontigs based on the evidence of a single link; it requires two or more links to perform a join.

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