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Chimera detection

Chimeras are artifacts of PCR. These are formed during PCR cycles by the joining of two or more different parent DNA templates. If these chimeras are not removed they may be recognized as novel sequences during the alignment process and therefore mislead interpretation. At present there are no tools that can remove chimeras completely without throwing away non-chimeric sequences. Of the various tools available, UCHIME was found to perform better than ChimeraSlayer, which was the best program to detect chimeras before UCHIME was developed1. To remove chimeras from 454 sequences Perseus can also be used2.

Software: UCHIME, ChimeraSlayer, Perseus


  1. Edgar, Robert C., et al. “UCHIME improves sensitivity and speed of chimera detection.” Bioinformatics 27.16 (2011): 2194-2200. 

  2. Quince, Christopher, et al. “Accurate determination of microbial diversity from 454 pyrosequencing data.” Nature methods 6.9 (2009): 639.