Black Box Chimera Check (B2C2): a Windows-Based Software for Batch Depletion of Chimeras from Bacterial 16S rRNA Gene Datasets

Viktoria Gontcharova 1, 2, Eunseog Youn 4, Randall D Wolcott1, 2, 3, Emily B Hollister5, Terry J Gentry 5, Scot E Dowd1, 2, *
1 Research and Testing Laboratory of the South Plains, Lubbock, TX, USA 79407
2 Medical Biofilm Research Institute, Lubbock, TX, USA 79407
3 Southwest Regional Wound Care Clinic, Lubbock, TX, USA 79410
4 Computer Science Department, Texas Tech University, Lubbock, TX, USA 79409-3104
5 Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, USA 77843-2474

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© Gontcharova et al.; Licensee Bentham Open.

open-access license: This is an open access article licensed under the terms of the Creative Commons Attribution Non-Commercial License ( which permits unrestricted, non-commercial use, distribution and reproduction in any medium, provided the work is properly cited.

* Address correspondence to this author at the Research and Testing Laboratory of the South Plains, Lubbock, TX, USA 79407; Tel: 806-771-1134; Fax: 806-771-1168;


The existing chimera detection programs are not specifically designed for "next generation" sequence data. Technologies like Roche 454 FLX and Titanium have been adapted over the past years especially with the introduction of bacterial tag-encoded FLX/Titanium amplicon pyrosequencing methodologies to produce over one million 250-600 bp 16S rRNA gene reads that need to be depleted of chimeras prior to downstream analysis. Meeting the needs of basic scientists who are venturing into high-throughput microbial diversity studies such as those based upon pyrosequencing and specifically providing a solution for Windows users, the B2C2 software is designed to be able to accept files containing large multi-FASTA formatted sequences and screen for possible chimeras in a high throughput fashion. The graphical user interface (GUI) is also able to batch process multiple files. When compared to popular chimera screening software the B2C2 performed as well or better while dramatically decreasing the amount of time required generating and screening results. Even average computer users are able to interact with the Windows .Net GUI-based application and define the stringency to which the analysis should be done. B2C2 may be downloaded from

Keywords: Chimera, chimera detection, high throughput, pyrosequencing, Windows, next generation.