Base Caller with Vocabulary

The Base Calling with Vocabulary (BCV) software package is intended for analysis of direct (population) sequencing chromatograms using known vocabulary sequences similar to the target DNA. BCV is designed for characterizing the bacterial populations in clinical samples from body sites or liquids that are normally sterile. The current version of BCV can only process chromatogram files obtained on Applied Biosystems capillary sequencing machines (ABI file format). In principle, the method can be applied to other sequencing platforms except high-throughput sequencing; however, the current software version has not been tested for such applications.

The BCV package has the following functionalities:

• Base calling: determining the sequence of IUPAC codes corresponding to sets of 1-4 nucleotides at each position for a chromatogram
• Indel detection: detecting insertions or deletions (indels) in components of the the DNA sample mixture relative to the main consensus sequence of the major pool of DNA variants
• Mixture deconvolution: determining the sequences of the sample components

The BCV software is distributed under the GNU GPL v. 3 license, and was successfully compiled on Linux and Windows Cygwin platforms.

To enjoy the full functionality of BCV, download and install it locally.

For base calling, mixture deconvolution and taxonomic assignment of 16S rRNA mixed chromatograms, use BCV online.

In case of any questions concerning BCV online, please contact us at bcv.pipeline@gmail.com